Systems and methods for detecting a biological condition

ABSTRACT

The present invention provides self-contained systems, apparatus and methods for determining a chemical state, the system includes a stationary cartridge for performing the assay therein, the cartridge adapted to house at least one reagent adapted to react with a sample; and at least one reporter functionality adapted to report a reaction of the at least one reagent with the sample to report a result of the assay, a mechanical controller including a first urging means adapted to apply a force externally onto the cartridge to release the at least one reagent; and at least one second urging means adapted to apply a removable force to induce fluidic movement in a first direction in the cartridge and upon removal of the force causing fluidic movement in an opposite direction to the first direction, an optical reader adapted to detect the reaction and a processor adapted to receive data from the optical reader and to process the data to determine said chemical state.

CROSS REFERENCE TO RELATED APPLICATIONS

The present invention claims priority from US provisional patentapplication 61/737,854, to Kasdan et al, filed on Dec. 17, 2012, U.S.provisional patent application 61/737,856, to Kasdan et al., filed onDec. 17, 2012 and from U.S. patent application Ser. No. 13/716,246 filedon Dec. 17, 2012, incorporated herein by reference.

FIELD OF THE INVENTION

The present invention relates generally to apparatus and methods fordetecting a biological condition, and more specifically to methods andapparatus for detecting a biological condition in small fluid samples.

BACKGROUND OF THE INVENTION

There are numerous medical conditions which are hard to diagnose. Oftendiagnosis by a physician is based on the physician's observation ofcombinations of symptoms in a patient. This sometimes, leads tomisdiagnosis. Furthermore, the patient's response to a treatment,whether drug or other modality is often followed up by physician'sobservation.

Many laboratory tests are performed in the diagnostic arena on a bodilyspecimen or fluid to determine a biological condition in a patient.However, these tests are performed off-line in diagnostic laboratories.Often, the laboratory services are only provided during a single 8-hourshift during the day and tend to be labor intensive. Some prior artpublications in the field include, inter alia, U.S. Pat. No. 8,116,984,US2006215155 and US2012187117.

Despite the inventions mentioned hereinabove, there still remains anunmet need to provide improved apparatus and methods for detecting anddiagnosing biological conditions in a patient.

SUMMARY OF THE INVENTION

It is an object of some aspects of the present invention to provideimproved apparatus and methods for detecting and diagnosing biologicalconditions in a patient.

In some embodiments of the present invention, improved methods,apparatus and kits are provided for detecting and diagnosing abiological condition in a patient.

In other embodiments of the present invention, a method and kit isdescribed for providing rapid detection of biological moieties in asample from a patient.

In further embodiments of the present invention, a method and kit isdisclosed for providing detection of biological moieties in a smallfluid sample from a patient.

There is thus provided according to an embodiment of the presentinvention, a self-contained system for performing an assay fordetermining a chemical state, the system including;

-   -   a) a stationary cartridge for performing the assay therein, the        cartridge adapted to house at least one reagent adapted to react        with a sample; and at least one reporter functionality adapted        to report a reaction of the at least one reagent with the sample        to report a result of the assay;    -   b) a mechanical controller including;        -   i. a first urging means adapted to apply a force externally            onto the cartridge to release the at least one reagent;        -   ii. at least one second urging means adapted to apply a            removable force to induce fluidic movement in a first            direction in the cartridge and upon removal of the force            causing fluidic movement in an opposite direction to the            first direction;    -   c) an optical reader adapted to detect the reaction; and    -   d) a processor adapted to receive data from the optical reader        and to process the data to determine the chemical state.

Additionally, according to an embodiment of the present invention, thecartridge further includes an alignment means adapted to align a readingchannel on the cartridge for a detection of the least one reporterfunctionality.

Furthermore, according to an embodiment of the present invention, thecartridge further comprises a plurality of fluidic open channels, allthe channels in liquid communication with each other.

Moreover, according to an embodiment of the present invention, thecartridge is adapted to be sealed after receiving a fluid specimen andto pass a predetermined quantity of the sample through at least part ofthe plurality of fluidic open channels.

Further, according to an embodiment of the present invention, thecartridge further includes at least one inflatable deformable elasticchamber adapted to apply at least one of a negative pressure and apositive pressure in the fluidic channels.

Additionally, according to an embodiment of the present invention, theat least one deformable elastic chamber is adapted to further contactthe at least one reagent stored in a sealed on-board storage chamberwith a predetermined quantity of the sample in a reaction chamber toinduce the reaction.

Further, according to an embodiment of the present invention, the afirst urging means is disposed proximal to the on-board storage chambersuch that upon movement is adapted to break a frangible seal on thestorage chamber.

Yet further, according to an embodiment of the present invention, thealignment means adapted to align with a reading channel on the cartridgefor a detection of a reaction in the predetermined quantity of thesample.

Additionally, according to an embodiment of the present invention, someof the plurality of fluidic open channels is of a cross-section of 0.1to 2 mm².

Notably, according to an embodiment of the present invention, thepredetermined quantity is of a volume of 10 to 500 microliters.

Furthermore, according to an embodiment of the present invention, thecartridge is adapted to contact a plurality of on-board reagents withthe at least one of the sample and a reaction product.

In some cases, according to an embodiment of the present invention, thecartridge is adapted to induce cascaded sequential reactions of theplurality of on-board reagents, with the at least one of the sample andthe reaction product.

Additionally, according to an embodiment of the present invention, thecartridge includes at least one reaction chamber of a volume of 200 to10000 microliters.

Furthermore, according to an embodiment of the present invention, thesystem further includes a temperature control device external to thecartridge, the device being adapted to control a temperature of thereaction.

Additionally, according to an embodiment of the present invention, thecartridge has a shelf-life of 6 to 24 months.

Importantly, according to an embodiment of the present invention, thecartridge is valveless.

Notably, according to an embodiment of the present invention, the assayis a flow cytometric assay.

Additionally, according to an embodiment of the present invention, thechemical state is a biochemical state.

Furthermore, according to an embodiment of the present invention, thebiochemical state is indicative of a biological condition.

Additionally, according to an embodiment of the present invention, thesample is a biological sample.

In some cases, according to an embodiment of the present invention, thebiological sample is a bodily sample.

Moreover, according to an embodiment of the present invention, thebodily sample is selected from a the group consisting of blood, serum,plasma, urine, saliva, cerebrospinal fluid (CSF), serous fluid,peritoneal fluid and synovial fluid blood, urine, plasma, serum andsaliva.

Additionally, according to an embodiment of the present invention, thecartridge is valveless.

Further, according to an embodiment of the present invention, thecartridge is a disposable microfluidics cartridge.

Yet further, according to an embodiment of the present invention, thesample is introduced to the cartridge via capillary action.

Additionally, according to an embodiment of the present invention, thecartridge includes at least one of the following elements;

-   -   i. a reservoir;    -   ii. a pump;    -   iii. a conduit;    -   iv. a miniaturized flow cell;    -   v. a transport channel;    -   vi. a reading channel;    -   vii. a microfluidic element;    -   viii. a compressed gas holding element;    -   ix. a compressed gas releasing element;    -   x. a nozzle element;    -   xi. a mixing element;    -   xii. a bellows element.    -   xiii. software adapted to activate the elements according to a        specific sequence; and    -   xiv. hardware to activate the elements according to a specific        sequence.

Additionally, according to an embodiment of the present invention, theat least one reagent disposed in the cartridge includes at least one of;

-   -   a. at least one target antibody;    -   b. at least one positive control identifying antibody; and    -   c. at least one negative control identifying detection moiety.

Moreover, according to an embodiment of the present invention, the atleast one reagent disposed in the cartridge includes at least onereference composition including at least one of;

-   -   a. a target signal reference composition; and    -   b. a reference identifier composition.

Additionally, according to an embodiment of the present invention, theat least one reagent disposed in the cartridge includes at least one of;

-   -   a. a positive control moiety; and    -   b. a negative control moiety.

Furthermore, according to an embodiment of the present invention, the atleast one reagent disposed in the cartridge includes at least one sepsisbiomarker.

There is thus provided according to another embodiment of the presentinvention, a method for determining a biological condition in a subject,the method including;

-   -   a. incubating a sample from the subject in the system described        herein for a predetermined period of time; and    -   b. receiving an indication responsive to the at least one        reporter functionality thereby providing an indication of the        biological condition in the subject in accordance with the        chemical state.

Additionally, according to an embodiment of the present invention, thebiological condition is selected from blood diseases such as leukemia,thrombocytopenia, immune system disorders, local infections, urinarytract disorders, autoimmune diseases and sepsis.

Furthermore, according to an embodiment of the present invention, theindication is quantitative.

Moreover, according to an embodiment of the present invention, themethod is completed within twenty minutes.

There is thus provided according to another embodiment of the presentinvention, a method for determining a biological condition in amammalian subject, the method including;

-   -   a. incubating a specimen from the subject with at least one        composition in a system described herein, for a predetermined        period of time to form at least one reaction product, when the        subject has the biological condition; and    -   b. receiving an indication of the at least one reaction product        responsive to at least one reporter element in the system        thereby providing the indication of the biological condition in        the subject.

There is thus provided according to another embodiment of the presentinvention, an automated method of determining the presence or absence ofsepsis in a subject, including;

-   -   a. contacting a blood sample from the subject with a        fluorescently-labeled binding moiety in the system as described        herein, the moiety specific to a sepsis marker, wherein the        volume of the blood sample is 50 μL or smaller; and    -   b. detecting the presence, absence or level of the binding        moiety in the sample, thereby determining the presence or        absence of sepsis in the subject within twenty minutes.

Furthermore, according to an embodiment of the present invention,wherein the sepsis marker is CD64.

Additionally, according to an embodiment of the present invention, thesepsis marker is CD163.

Moreover, according to an embodiment of the present invention, themethod further includes contacting the blood sample with a secondfluorescently-labeled binding moiety specific for a second sepsismarker.

Further, according to an embodiment of the present invention, the sepsismarker is CD64 and the second sepsis marker is CD163.

There is thus provided according to another embodiment of the presentinvention, a method for performing an assay for determining a chemicalstate in a self-contained stationary cartridge, the method including;

-   -   a. introducing a sample into the system described herein;    -   b. reacting at least one reagent with the sample; and    -   c. detecting a signal associated with at least one reporter        functionality, the at least one reporter functionality adapted        to report a reaction of the at least one reagent with the        sample, thereby determining the chemical state.

Furthermore, according to an embodiment of the present invention, themethod further includes forming at least one product and detecting asignal associated with the product.

Additionally, according to an embodiment of the present invention theassay is a flow cytometric assay.

Further, according to an embodiment of the present invention, thechemical state is a biochemical state.

Further, according to an embodiment of the present invention, thebiochemical state is indicative of a biological condition.

Furthermore, according to an embodiment of the present invention, thesample is a biological sample.

Additionally, according to an embodiment of the present invention, thebiological sample is a bodily sample.

Furthermore, according to an embodiment of the present invention, thebodily sample is selected from the group consisting of blood, serum,plasma, urine, saliva, cerebrospinal fluid (CSF), serous fluid,peritoneal fluid and synovial fluid.

Moreover, according to an embodiment of the present invention, the atleast one reagent includes at least one of;

-   -   a. a cell surface marker;    -   b. a cell stain;    -   c. a reagent bound to a solid support;    -   d. a chemical indicator; and    -   e. a biological cell indicator.

Furthermore, according to an embodiment of the present invention, thecell surface marker is selected from the group consisting of CD64, CD4,CD8, a stem cell indicator, a Minimal Residual Disease indicator and alymphocyte subtype indicator.

Additionally, according to an embodiment of the present invention, thecell stain is selected from the group consisting of a white blood celldifferential indicator, an apoptosis indicator.

Further, according to an embodiment of the present invention, thereagent bound to the solid support is selected from the group consistingof an immobilized enzyme, an immobilized substrate, a plasma proteinbead, an antibody bead, an antigen bead and an ELISA assay.

Additionally, according to an embodiment of the present invention, thechemical indicator is selected from the group consisting of a colorindicator, a turbidity indicator, a pH indicator, an adsorptionindicator, an emission indicator and a chemical reaction indicator.

Furthermore, according to an embodiment of the present invention, thebiological cell indicator is selected from the group consisting of acell cycle stage indicator, a cell proliferation indicator, a cytokineindicator, a metabolic indicator and an apoptosis indicator.

Further, according to an embodiment of the present invention, the atleast one reagent includes at least two reagents.

Moreover, according to an embodiment of the present invention, the atleast two reagents include at least one of;

-   -   a. a cell surface marker and a cell element stain;    -   b. a cell surface marker and a plasma protein bead assay;    -   c. a cell surface marker and a solution change marker;    -   d. a cell element stain and a plasma protein bead assay; and    -   e. a cell element stain and a solution change marker.

Furthermore, according to an embodiment of the present invention, thebiological condition is selected from blood diseases such as leukemia,thrombocytopenia immune system disorders, local infections, urinarytract disorders, autoimmune diseases and sepsis.

There is thus provided according to another embodiment of the presentinvention, a method for forming a chemical reaction in a stationarycartridge, the method including;

-   -   a. storing at least one composition in the cartridge described        herein; and    -   b. activating at least one inflatable chamber in the cartridge        to provide at least one pressure force to the at least one        reagent thereby inducing the chemical reaction.

There is thus provided according to an embodiment of the presentinvention, a kit for evaluating a biological condition in a patient, thekit comprising;

-   -   a) a disposable element for receiving a biological specimen and        for combining said specimen with at least one composition;    -   b) at least one composition comprising at least one detector        moiety adapted to react with said specimen to form a reaction        product, when said patient has said biological condition; and    -   c) at least one reporter element adapted to provide an        indication of reaction product thereby providing the indication        of the biological condition.

Additionally, according to an embodiment of the present invention, thekit further comprises;

-   -   d) instructions for using the kit.

Furthermore, according to an embodiment of the present invention, thedisposable element is a disposable cartridge.

Moreover, according to an embodiment of the present invention, thedisposable cartridge is a disposable microfluidics cartridge.

Additionally, according to an embodiment of the present invention, thedisposable microfluidics cartridge comprises at least one of thefollowing elements:

-   -   a) a reservoir;    -   b) a pump;    -   c) a conduit;    -   d) a miniaturized flow cell;    -   e) a transport channel;    -   f) a microfluidic element;    -   g) a compressed gas holding element;    -   h) a compressed gas releasing element;    -   i) a nozzle element;    -   j) a mixing element;    -   k) a bellows element;    -   l) software adapted to activate said elements according to a        specific sequence; and    -   m) hardware to activate said elements according to a specific        sequence.

Additionally, according to an embodiment of the present invention, thedisposable microfluidics cartridge comprises at least two of theelements.

Additionally, according to an embodiment of the present invention, thedisposable microfluidics cartridge comprises at least three of theelements.

Additionally, according to an embodiment of the present invention, thedisposable microfluidics cartridge comprises at least four of theelements.

Additionally, according to an embodiment of the present invention, thedisposable microfluidics cartridge comprises at least five of theelements.

Additionally, according to an embodiment of the present invention, thedisposable microfluidics cartridge comprises at least ten of theelements.

Additionally, according to an embodiment of the present invention, thedisposable microfluidics cartridge comprises at least twenty of theelements.

Additionally, according to an embodiment of the present invention, thedisposable microfluidics cartridge comprises at least thirty of theelements.

According to an embodiment of the present invention, the microfluidicskit is configured to provide the rapid indication with one hour.

According to another embodiment of the present invention, themicrofluidics kit is configured to provide the rapid indication withthirty minutes.

According to another embodiment of the present invention, themicrofluidics kit is configured to provide the rapid indication withfifteen minutes.

According to another embodiment of the present invention, themicrofluidics kit is configured to provide the rapid indication with tenminutes.

According to another embodiment of the present invention, themicrofluidics kit is configured to provide the rapid indication withfive minutes.

According to another embodiment of the present invention, themicrofluidics kit is configured to provide the rapid indication with oneminute.

According to another embodiment of the present invention, themicrofluidics kit is configured to provide the rapid indication withthirty seconds.

According to another embodiment of the present invention, themicrofluidics kit is configured to provide the rapid indication with tenseconds.

According to another embodiment of the present invention, themicrofluidics kit is configured to provide the rapid indication with onesecond.

There is thus provided according to an embodiment of the presentinvention, a microfluidics assay kit for performing a rapid biologicalassay, the kit comprising;

-   -   a) a disposable element comprising a reactant, the disposable        element being adapted to receive a sample comprising a        biological entity and for combining said reactant with said        biological entity to form a reaction product; and    -   b) at least one reporter element adapted to provide a rapid        indication of disappearance of said reactant thereby providing        rapid assay of the biological entity.

There is thus provided according to an embodiment of the presentinvention, a microfluidics assay kit for performing a rapid assay of abiological entity, the kit comprising;

-   -   a) a disposable element comprising a reactant, the disposable        element being adapted to receive a sample comprising the        biological entity and for combining said reactant with said        biological entity to form a reaction product; and    -   b) at least one reporter element adapted to provide a rapid        indication of appearance of said reaction product thereby        providing rapid assay of the biological entity.

There is thus provided according to an embodiment of the presentinvention, a composition for evaluating a biological condition, thecomposition comprising;

-   -   a. a sample composition comprising at least one of;        -   i. a bodily specimen comprising a target moiety;        -   ii. a positive control moiety; and        -   iii. a negative control moiety;    -   b. a detection composition comprising at least one of;        -   i. at least one target antibody;        -   ii. at least one positive control identifying antibody; and        -   iii. at least one negative control identifying detection            moiety or characteristic; and    -   c. at least one reference composition comprising at least one        of;        -   i. a target signal reference composition; and        -   ii. a reference identifier composition.

There is thus provided according to another embodiment of the presentinvention a composition for evaluating a biological condition, thecomposition comprising;

-   -   a. a sample composition comprising at least one of;        -   iii. a bodily specimen comprising a target moiety;        -   iv. a positive control moiety; and        -   v. a negative control moiety;    -   b. an antibody composition comprising at least one of;        -   vi. at least one target antibody (CD64 antibody);        -   vii. at least one positive control identifying antibody            (CD163); and        -   viii. at least one negative control identifying antibody or            characteristic; and    -   c. at least one reference composition comprising at least one        of;        -   ix. a target signal reference composition; and        -   x. a reference identifier composition.

Additionally, according to an embodiment of the present invention, thecomposition further comprises at least one conditioning moietycomprising;

-   -   d. at least one lysis reagent; and    -   e. at least one diluent.

Furthermore, according to an embodiment of the present invention, thebiological condition is selected from a group consisting of blooddiseases such as leukemia, thrombocytopenia immune system disorders,local infections, urinary tract disorders, autoimmune diseases andsepsis.

Moreover, according to an embodiment of the present invention the bodilyspecimen is selected from a group consisting of blood, serum, plasma,urine, saliva, cerebrospinal fluid (CSF), serous fluid, peritoneal fluidand synovial fluid.

According to another embodiment of the present invention, the targetmoiety includes a CD64 surface antigen on neutrophils.

Additionally, according to a further embodiment of the presentinvention, the positive control moiety includes monocytes and thenegative control includes lymphocytes.

Additionally, according to an embodiment of the present invention, thetarget moiety is CD64 on neutrophils, the positive control moietyincludes CD64 expression on monocytes, and the negative control moietyincludes lymphocytes without CD64 expression.

Further, according to an embodiment of the present invention, the targetindicator is bound to a signaling moiety on the at least one targetantibody.

Yet further, according to an embodiment of the present invention, the atleast one reference composition includes beads.

Additionally, according to an embodiment of the present invention, thebeads include polystyrene microbeads.

Moreover, according to an embodiment of the present invention, thetarget antibody reference composition includes a first fluorescentsignal and the reference identifier composition includes a secondfluorescent signal.

Furthermore, according to an embodiment of the present invention, thefirst fluorescent signal includes FITC and the second fluorescent signalincludes Starfire Red fluor.

There is thus provided according to an embodiment of the presentinvention, a method of quantifying a biomarker in a sample, comprising;

-   -   a. contacting the sample with a fluorescently-labeled binding        moiety that specifically binds to the biomarker;    -   b. detecting a first fluorescent signal from at least a portion        of the labeled sample;    -   c. detecting a second fluorescent signal from a population of        fluorescently-labeled particles, wherein the population includes        a known fluorescent intensity over a fixed time; and    -   d. normalizing the first fluorescent signal to the second        fluorescent signal, thereby quantifying the biomarker, wherein        the normalizing includes using a device comprising software        capable of comparing the first and second fluorescent signal.

Furthermore, according to an embodiment of the present invention, thebiomarker is a sepsis biomarker.

Moreover, according to an embodiment of the present invention, thebiomarker is CD64 or CD163.

Additionally, according to an embodiment of the present invention, thesample is a blood sample.

According to another embodiment of the present invention, thefluorescent label of the binding moiety and the fluorescent label of theparticles is the same fluorescent label.

Further, according to an embodiment of the present invention, thebinding moiety is an antibody.

According to an embodiment of the present invention, the software iscapable of recognizing a specific lot of fluorescently-labeledparticles.

Moreover, according to an embodiment of the present invention, theindividual fluorescent signals include at least one first fluorescentsignal and at least one second fluorescent signal.

Additionally, according to an embodiment of the present invention thefluorescently-labeled binding moiety targets a first cell population anda second cell population in the sample.

According to another embodiment of the present invention the detectionof binding of the binding moiety to the second cell population providesan internal positive control for the sample.

Furthermore, according to an embodiment of the present invention, thebinding moiety is anti-CD64 antibody and the first cell populationincludes polymorphonuclear leukocytes.

Yet further, according to an embodiment of the present invention, thesecond cell population includes monocytes.

According to an embodiment of the present invention, the method furthercomprises the step of determining the presence of at least one cellpopulation in the sample that is not bound by the binding moiety, thusproviding an internal negative control for the sample.

There is thus provided according to another embodiment of the presentinvention a composition for evaluating a biological condition, thecomposition comprising;

-   -   a. a sample comprising at least one of;        -   i. a bodily specimen comprising a target moiety;        -   ii. a positive control moiety; and        -   iii. a negative control moiety;    -   b. an antibody composition comprising at least one of;        -   iv. at least one target antibody;        -   v. at least one positive control identifying antibody; and        -   vi. at least one negative control identifying antibody or            characteristic; and    -   c. at least one reference composition comprising at least one        of;        -   vii. a target antibody reference composition; and        -   viii. a reference identifier composition.

According to an embodiment of the present invention, the compositionfurther comprises at least one conditioning moiety comprising;

-   -   a) at least one lysis reagent; and    -   b) at least one diluent.

There is thus provided according to another embodiment of the presentinvention, a method of determining the presence or absence of sepsis ina subject, the method including;

-   -   a) contacting a blood sample from the subject with a        fluorescently-labeled binding moiety specific to a sepsis        marker, wherein the volume of the blood sample is 50 μL or        smaller; and    -   b) detecting the presence, absence or level of the binding        moiety in the sample, thereby determining the presence or        absence of sepsis in the subject.

There is thus provided according to another embodiment of the presentinvention, a method of quantifying a biomarker in a sample, comprising;

-   -   a) contacting the sample with a fluorescently-labeled binding        moiety that specifically binds to the biomarker;    -   b) detecting a first fluorescent signal from at least a portion        of the labeled sample;    -   c) detecting a second fluorescent signal from a population of        fluorescently-labeled particles, wherein the population includes        a known fluorescent intensity over a fixed time; and    -   d) normalizing the first fluorescent signal to the second        fluorescent signal, thereby quantifying the biomarker, wherein        the normalizing includes using a device comprising software        capable of comparing the first and second fluorescent signal.

According to some embodiments, the sample may be liquid, according toother embodiments, the sample may be a colloid or suspension. Accordingto further embodiments, the sample may be a solid, such as in a powderor crystal form.

Typical turnaround times for diagnostic prior art assays are 30-120minutes. Often, the time lost in waiting for laboratory results can leadto a further deterioration in a patient, and sometimes death. In somecases, the physician has to act without having the laboratory results.This can lead to providing the patient with the wrong treatment. Thepresent invention provides rapid assays to save lives and provide fastcorrect treatments to a patient.

There is thus provided according to an embodiment of the presentinvention automated method of determining the presence or absence ofsepsis in a subject, including;

-   -   a) contacting a blood sample from the subject with a        fluorescently-labeled binding moiety specific to a sepsis        marker, wherein the volume of the blood sample is 50 μL or        smaller; and    -   b) detecting the presence, absence or level of the binding        moiety in the sample, thereby determining the presence or        absence of sepsis in the subject within twenty minutes.

Additionally, according to an embodiment of the present invention, thesepsis marker is CD64.

Furthermore, according to an embodiment of the present invention, asecond sepsis marker is CD163.

Moreover, according to an embodiment of the present invention, themethod further includes contacting the blood sample with a secondfluorescently-labeled binding moiety specific for a second sepsismarker.

Further, according to an embodiment of the present invention, the sepsismarker is CD64 and the second sepsis marker is CD163.

Additionally, according to an embodiment of the present invention, thebinding moiety is an antibody.

Moreover, according to an embodiment of the present invention, thedetecting step is performed in a device capable of receiving the sampleand capable of detecting the binding moiety.

Additionally, according to an embodiment of the present invention, themethod further includes the step of calibrating the device by detectinga population of the fluorescently-labeled particles.

According to another embodiment of the present invention, the particlesinclude the same fluorescent label as the fluorescently-labeled bindingmoiety.

Additionally, according to an embodiment of the present invention, themethod further includes a second population of particles that includethe same fluorescent label as the second fluorescently-labeled bindingmoiety.

Moreover, according to an embodiment of the present invention, themethod further includes performing an internal calibration after thedetecting the fluorescently-labeled binding moiety.

Notably, according to an embodiment of the present invention, thecalibration is completed in less than 5 minutes.

According to some embodiments, the particles are microbeads.

Additionally, according to an embodiment of the present invention, themethod is performed in less than 15 minutes.

Furthermore, according to an embodiment of the present invention, themethod, further includes the step of determining the presence of atleast one cell population in the sample that is not bound by the bindingmoiety, thus providing an internal negative control for the sample.

The present invention will be more fully understood from the followingdetailed description of the preferred embodiments thereof, takentogether with the drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention will now be described in connection with certain preferredembodiments with reference to the following illustrative figures so thatit may be more fully understood.

With specific reference now to the figures in detail, it is stressedthat the particulars shown are by way of example and for purposes ofillustrative discussion of the preferred embodiments of the presentinvention only and are presented in the cause of providing what isbelieved to be the most useful and readily understood description of theprinciples and conceptual aspects of the invention. In this regard, noattempt is made to show structural details of the invention in moredetail than is necessary for a fundamental understanding of theinvention, the description taken with the drawings making apparent tothose skilled in the art how the several forms of the invention may beembodied in practice.

In the drawings:

FIG. 1A is a simplified three dimensional front view of a system fordetecting a biological condition, in accordance with an embodiment ofthe present invention;

FIG. 1B is a simplified three dimensional inner front view of a readerassembly for detecting a biological condition, in accordance with anembodiment of the present invention;

FIG. 1C is a simplified three dimensional inner rear view of a readerassembly for detecting a biological condition, in accordance with anembodiment of the present invention;

FIG. 2A is a simplified blown up diagram of an optical reader assemblyfor detecting a biological condition, in accordance with an embodimentof the present invention;

FIG. 2B is another simplified blown up diagram of a photomultiplier tubeof the optical reader assembly for detecting a biological condition, inaccordance with an embodiment of the present invention;

FIG. 3A shows a reader optics assembly, a cartridge handling unit, and aforward scatter detection unit, in accordance with an embodiment of thepresent invention;

FIG. 3B shows a right side view of a reader optics assembly, inaccordance with an embodiment of the present invention;

FIG. 3C shows a left side view of a reader optics assembly, inaccordance with an embodiment of the present invention;

FIG. 3D is a forward scatter detection assembly, in accordance with anembodiment of the present invention;

FIG. 3E is a side view of the forward scatter detection assembly, inaccordance with an embodiment of the present invention;

FIG. 4A shows a cutaway view of a reader assembly, in accordance with anembodiment of the present invention;

FIG. 4B shows an exploded right side view of a reader assembly, inaccordance with an embodiment of the present invention;

FIG. 4C shows a left side blown up view of the reader assembly, inaccordance with an embodiment of the present invention;

FIG. 4D shows a rear view of a cartridge handling unit (CHU), inaccordance with an embodiment of the present invention;

FIG. 4E shows a front view of a cartridge handling unit (CHU), inaccordance with an embodiment of the present invention;

FIG. 5 shows an exploded view of a reader optics assembly, in accordancewith an embodiment of the present invention;

FIG. 6 is a simplified illustration of a disposable cartridge of thesystem of FIG. 1A, in accordance with an embodiment of the presentinvention;

FIG. 7A is a simplified schematic illustration of an optical arrangementof a reader optics assembly, in accordance with an embodiment of thepresent invention;

FIG. 7B is another simplified schematic illustration of opticalarrangement of a reader optics assembly, in accordance with anembodiment of the present invention;

FIG. 8A is a schematic representation of one example of multi-wavelengthexcitation in the optical unit of FIG. 7A or 7B, in accordance with anembodiment of the present invention;

FIG. 8B shows a graphical output of transmission as a function ofwavelength for a dichroic filter of FIG. 7B, employing themulti-wavelength excitation of FIG. 8A, in accordance with an embodimentof the present invention;

FIG. 8C is a schematic representation of part of the optical unitemploying multi-wavelength excitation of FIG. 8A and the dichroic filterof FIG. 5B, in accordance with an embodiment of the present invention.

FIG. 9A is a schematic view of a sampling cartridge of the system ofFIG. 1A, in accordance with an embodiment of the present invention;

FIG. 9B shows a schematic view of disposable cartridge in flow-cytometerdevice, in accordance with an embodiment of the present invention;

FIG. 10 is a simplified flowchart of a method for rapid determination ofa medical condition, in accordance with an embodiment of the presentinvention;

FIG. 11 is a three-dimensional graph showing the optical output overtime of reference beads (RM) relative to a sample from a human patient(PMN), in accordance with an embodiment of the present invention;

FIGS. 12A-12C show graphs of optical outputs over time of the referencebeads and the sample from a human patient, in accordance with anembodiment of the present invention;

FIG. 13A is an outer side view of a cartridge assembly, in accordancewith an embodiment of the present invention;

FIG. 13B is an inner side view of a cartridge assembly, in accordancewith an embodiment of the present invention;

FIG. 14A-14O show a sequence of process events in a cartridge assembly,in accordance with an embodiment of the present invention;

FIG. 15 is a schematic illustration of a micro flow spectrometerreading, in accordance with an embodiment of the present invention;

FIG. 16 is a flow chart of a method for optical processing, inaccordance with an embodiment of the present invention;

FIGS. 17A-17B are schematic illustrations of steps of use of a graphicaluser interface, in accordance with an embodiment of the presentinvention;

FIG. 18 is a cartridge block diagram showing a role of signal processingsoftware, in accordance with an embodiment of the present invention;

FIG. 19A is a flow chart of an algorithm for biological detection, inaccordance with an embodiment of the present invention;

FIG. 19B is a flow chart of an algorithm for biological detection, inaccordance with an embodiment of the present invention;

FIGS. 20A-20B shows bandwidth leveled and smoothed arrays, in accordancewith an embodiment of the present invention;

FIGS. 21A-21B are schematics for solving a fluor decomposition of anobserved signal, in accordance with an embodiment of the presentinvention;

FIGS. 22A-22B is a graphical comparison of system performance with FITCbeads with MESF detection versus FACS, in accordance with an embodimentof the present invention;

FIGS. 23A-23B show graphical displays of linearity of system performancewith Alexa 488 MESF, in accordance with an embodiment of the presentinvention;

FIG. 24 is a three-dimensional graph showing the optical output overtime of a CD4-CD8 assay, in accordance with an embodiment of the presentinvention;

FIG. 25 is a graphical display showing a cluster analysis of a CD4-CD8assay, in accordance with an embodiment of the present invention;

FIGS. 26-27 are graphical displays showing cluster separations of thecluster analysis of FIG. 25, in accordance with an embodiment of thepresent invention; and

FIG. 28 is a comparison table of different array options, in accordancewith an embodiment of the present invention;

FIG. 29A is a flowchart of a specific implementation of an algorithm forselecting groups of data from a scatterplot, in accordance with anembodiment of the present invention;

FIG. 29B is a flowchart of a general implementation of an algorithm forselecting groups of data from a scatterplot, in accordance with anembodiment of the present invention;

FIG. 30 is a scatterplot matrix of the four fluors signatures showingfour distinct event groups, in accordance with an embodiment of thepresent invention;

FIG. 31A is a histogram of data of Starfire Red (SFR) signature values,in accordance with an embodiment of the present invention;

FIG. 31B is a plot of a polynomial and first and second derivativethereof of the histogram shown in FIG. 31A, in accordance with anembodiment of the present invention;

FIG. 32A is a histogram of data of PE488 signature values, in accordancewith an embodiment of the present invention;

FIG. 32B shows a polynomial fitted to the histogram in FIG. 32A as wellas corresponding first and second derivatives, in accordance with anembodiment of the present invention;

FIG. 33A is a histogram of data of PEAF488 signature values, inaccordance with an embodiment of the present invention;

FIG. 33B shows a polynomial fitted to the histogram in FIG. 33A as wellas corresponding first and second derivatives, in accordance with anembodiment of the present invention.

FIG. 34A is a histogram of data of Diode 1 channel signature values, inaccordance with an embodiment of the present invention; and

FIG. 34B shows the polynomial fitted to the histogram in FIG. 34A aswell as the corresponding first and second derivatives, in accordancewith an embodiment of the present invention.

In all the figures similar reference numerals identify similar parts.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

In the detailed description, numerous specific details are set forth inorder to provide a thorough understanding of the invention. However, itwill be understood by those skilled in the art that these are specificembodiments and that the present invention may be practiced also indifferent ways that embody the characterizing features of the inventionas described and claimed herein.

International patent application publication no. WO2011/128893 to Kasdanet al., describes a device, system and method for rapid determination ofa medical condition and is incorporated herein by reference.

Reference is now made to FIG. 1A, which is a simplified threedimensional front view of a system 101 comprising a reader assembly 100and a cartridge 110 for detecting a biological condition, in accordancewith an embodiment of the present invention.

Shown in FIG. 1A are the reader assembly 100 and the cartridge 110. Thecartridge is inserted in the reader assembly as shown. Once thecartridge is inserted in the reader assembly all assay pre-analyticalprocessing and analysis are performed automatically. Results of theanalysis are displayed on a user interface touchscreen 115, which isalso used to control operation of the reader.

FIG. 1B shows a simplified three dimensional inner front view 103 ofreader assembly 100 for detecting a biological condition, in accordancewith an embodiment of the present invention.

The internal components of the reader assembly are shown in FIG. 1B.There is seen left side view 120, showing an ITX computer, 122, a Galilmotor controller, 124, an electronics power supply 126, cartridge, 110,inserted into a cartridge handling unit (CHU) 128 and a forward scatterdetector 130. Also seen, is a right side view 140 showing reader optics142, a data acquisition board 144 and a general electronics printedcircuit board 146.

Reference is now made to FIG. 2A, which is a simplified blown up diagramof a reader optics assembly 200 for detecting a biological condition, inaccordance with an embodiment of the present invention. FIG. 2B isanother simplified blown up diagram of a photomultiplier tube 250 of theoptical reader assembly for detecting a biological condition, inaccordance with an embodiment of the present invention.

FIG. 2A shows the main modular components of a reader optics assembly200. A complete side view 220 of the optical assembly is seen, inaddition to a top view 222. A laser unit 203 includes a laser and beamexpander 223 in its heat sink assembly 221. The assembly furthercomprises an excitation and emission collection optics 204. The readeroptics assembly also comprises a photomultiplier assembly 202, a lasermirror cover 205, a PMT mirror cover 206, a modified M6 set screw 207, abox clamp 208, and various screws 209-211. The reader optics assembly isassembled as shown in FIG. 2A.

FIG. 2B shows details of the PMT assembly. A side view and an end viewof the PMT assembly are shown as side view 270 and end view 272respectively. The major elements of the PMT assembly include a PMT box251, a PMT grating assembly 252, a PMT bridge assembly 255, a PMT cover258, a PMT unit 259, a PMT lens assembly 260, a PMT pinhole nut 261, apinhole 262, a pinhole hood 263 and an adjustment bar 265.

FIG. 3A shows a reader optics assembly 310, a cartridge handling unit312 and a forward scatter detection unit 314, in accordance with anembodiment of the present invention.

FIG. 3B shows a right side view of a complete reader optics assembly142, in accordance with an embodiment of the present invention.

FIG. 3C shows a left side view of the reader optics assembly, inaccordance with an embodiment of the present invention.

FIG. 3D is a forward scatter detection assembly 130, in accordance withan embodiment of the present invention. This assembly contains LEDs,352, to illuminate a reading channel (such as reading channel 1452 (FIG.14M) during an autofocus process, a stop 358, to block low angle scatterand a lens 356 to collect the desired forward scatter for the detectionphotodiode. (forward scatter detector 130, FIG. 1B).

FIG. 3E is a side view of forward scatter detection assembly 130, inaccordance with an embodiment of the present invention. Shown in thisview are an illumination lens 350, collection lenses 356, 357, and 358,as well as a detection photodiode 360.

FIG. 4A shows a cutaway view of reader assembly 130, in accordance withan embodiment of the present invention. This is cutaway view of thereader assembly showing its components in its front and on a left side.These components include an ITX board 122, a cartridge handling unit128, and the forward scatter detection assembly, 130.

FIG. 4B shows an exploded right side view of a reader assembly 129, inaccordance with an embodiment of the present invention. The three majorcomponents in this view are a reader optics assembly 142, a cartridgehandling unit 128, and a forward scatter detection module 130.

FIG. 4C shows a left side blown up view of the reader assembly, inaccordance with an embodiment of the present invention. Shown in thisview are ITX computer board 122, cartridge handling unit 128, forwardscatter detection assembly 130, and the other side of the reader opticsassembly, 142.

FIG. 4D shows a rear view of cartridge handling unit (CHU) 128, inaccordance with an embodiment of the present invention. In this view, ahandle 199 of the inserted cartridge, 110, can be seen. Sensors 412 areconfigured therein to detect the position of motors 410, and actuators414, which are adapted to crush the blisters, as well as an actuator 416(940, FIG. 9, 1415, 1417 FIGS. 14A-L), can be seen on the shafts 417 ofthe motor. An opening 418 is provided for the microscope objective 438to view the reading channel on the cartridge.

FIG. 4E shows a front view of a cartridge handling unit (CHU), inaccordance with an embodiment of the present invention. This figureshows the front view of the cartridge handling unit (CHU) 128. In thisview, the handle in the upper portion of cartridge 110 can be seen. Aport 420 to view the microfluidic path is provided. This port is viewedby a camera 430, in order to ensure that the correct operation occurswithin the cartridge. Another opening 441 is provided for the forwardscatter to exit the cartridge handling unit and be observed by theforward scatter detection assembly 130.

FIG. 5 shows an exploded view of a reader assembly 130, in accordancewith an embodiment of the present invention.

FIG. 6 is a simplified illustration of a disposable cartridge 6050 forrapid determination of a medical condition, in accordance with anembodiment of the present invention;

Disposable cartridge 6050 is adapted to receive a bodily fluid, such as,but not limited to, blood, urine, serum or plasma. The disposablecartridge is constructed and configured to have several differentsections 6052, 6054, 6056 and 6058. Section 6052 is a body fluidaspiration section, which is adapted to receive the body fluid directlyor indirectly from the patient (or animal) and this section acts as areservoir of the body fluid.

Disposable cartridge 6050 comprises fluid conveying means between thesections; such as, but not limited to, air pressure, liquid pressure,mechanical means and combinations thereof. Body fluid aspiration section6052 is adapted to convey a predetermined quantity of the body fluid (abody fluid sample 6051) to a pre-analytical sample processing section6054.

In pre-analytical sample processing section 6054, at least onepreparatory step is performed on the body fluid such as, but not limitedto:

-   -   a) incubation with at least one antibody;    -   b) incubation with at least one antigen;    -   c) staining of at least one cell type in the body fluid;    -   d) enzymatic lysing of at least one cell type of the body fluid;    -   e) osmotic lysing of at least one cell type of the body fluid;    -   l) heat or cool at least part of the bodily fluid;    -   g) addition of reference material to the bodily fluid; and    -   h) chemical reaction with at least one element of the body        fluid.

The pre-treated sample of bodily fluid is then conveyed frompre-analytical sample processing section 6054 to a sampleexcitation/interaction zone or section 6056. This pre-treated sample maybe conveyed continuously or in a batch mode to sampleexcitation/interaction section 6056.

FIG. 7A is a simplified schematic illustration of an optical arrangementof a reader optics assembly 400, in accordance with an embodiment of thepresent invention;

A laser 440 or other appropriate light source provides a light beam 442,which may be directed towards a plurality of optical elements, includinga dichroic filter 443, a beam splitter 444, a focusing lens 445, apinhole 446 and a silicon reader unit 447, for recording a signal from abeam 442 directed through the objective 438 towards a sample 450 andreturned to the optical unit. Additional optical elements may include anoptional attenuator 448, a high-pass filter 449, a focusing lens 451, aslit 452, a concave grating 453, and a PMT array 454. This arrangementof elements, representing an embodiment of the present invention, allowsfor generation of excitation light, focusing it on a sample, collectingreflected and emitted light signal resulting from the interaction of theexcitation light and fluorophores in the sample and recording saidreturned light so as to determine fluorescence of sample in response tolight illumination from laser 440.

With respect to FIG. 7A, the laser illumination 442 is reflected by thedichroic filter 443 through the objective 438 and focused on the channelcontaining the flowing particles 458. This illumination excites thefluorophores attached to the protein markers that are bound to thecells.

The resulting fluorescent illumination is collected by the objective 438and because of the longer wavelength of this emission passes through thedichroic filter 443 and is reflected by the beam splitter 444 throughthe high pass filter 449. The high pass filter blocks any reflectedlaser illumination. The focusing lens 451 focuses the multi-wavelengthemission illumination on the slit 452. The concave grating 453 imagesthe slit at multiple wavelengths on the elements of the PMT array 454.This completes the process of creating a multispectral detection of thefluorescent emission.

While most of the illumination collected by the objective is reflectedby the beam splitter 444 a small fraction is allowed to pass through andis focused by focusing lens 445 through a pinhole 446 on the siliconreader unit 447, which may be a single photodiode or a focal plane arraysuch as CCD sensor. During the focusing operation best focus is achievedwhen the signal on this reader unit 447 is maximized. When this signalis maximized, the intensity of the signal on the PMT array 454 is alsomaximized.

Reference is now made to FIG. 7B, which is another simplified schematicillustration of optical arrangement 460 of a reader optics assembly 400(FIG. 7A), in accordance with an embodiment of the present invention;

With respect to FIG. 7B, as in FIG. 7A, the laser illumination isreflected by the dichroic filter 472 through the objective 476 andfocused on the channel containing the flowing particles. Thisillumination excites the fluorophores attached to the protein markersthat are bound to the cells. The resulting fluorescent illumination iscollected by the objective 476 and because of the longer wavelength ofthis emission passes through the dichroic filter 472 and is reflected bythe beam splitter 468 through the high pass filter 470. The high passfilter 470 blocks any reflected laser illumination. The focusing lens466 focuses the multi-wavelength emission illumination on the slit 478.The concave grating 482 images the slit at multiple wavelengths on theelements of the PMT array 476. This completes the process of creating amultispectral detection of the fluorescent emission. While most of theillumination collected by the objective 476 is reflected by the beamsplitter 468 a small fraction is allowed to pass through and is focusedthrough a pinhole 464 on the silicon reader unit 462. During thefocusing operation best focus is achieved when the signal on this readerunit is maximized. When this signal is maximized, the intensity of thesignal on the PMT array 476 is also maximized.

FIG. 8A is a schematic representation of one example of multi-wavelengthexcitation in the optical unit of FIG. 7A or 7B, in accordance with anembodiment of the present invention;

Reference is now made to FIG. 8A, which is a schematic representation500 of one example of multi-wavelength excitation in the optical unit ofFIG. 7A or 7B, in accordance with an embodiment of the presentinvention. FIGS. 8A-8C show an extension of the optical configuration inFIGS. 7A and 7B, to allow multiple excitation wavelengths.

FIG. 8A shows the configuration for combining multiple lasers ofdifferent wavelengths to yield a single coaxial beam 514 containing allof the wavelengths. Two different wavelengths, such as green 502 and red506, may be combined using a dichroic mirror 504. One of the beams, red506 is reflected by the dichroic mirror, while the second beam, green502 passes through the dichroic mirror to yield a single beam 508,yellow, containing both wavelengths. This combined wavelength beam isnow used as one of the inputs to a second dichroic mirror 516 with thethird wavelength 512 being reflected by the second dichroic mirror toyield a single coaxial beam 510 containing all three wavelengths.

Reference is now made to FIG. 8B, which shows a graphical output 520 oftransmission as a function of wavelength for dichroic filter 500 of FIG.7B, employing the multi-wavelength excitation of FIG. 8A, in accordancewith an embodiment of the present invention.

A multiband dichroic mirror (not shown) similar, or identical to, mirror552 of FIG. 8C is used to illuminate the sample through an objective 554(FIG. 8C), while allowing the resulting emission to pass throughdichroic mirror 552 at all wavelengths, except those of multibeamexcitation 514 (FIG. 8A).

In this way the same epi-configuration used with a single wavelengthcan, in fact, be used with appropriate changes to dichroic mirror 552and the addition of multiple lasers 502, 506, 512 to providemulti-wavelength excitation, while maintaining virtually all of thedetection wavelengths of a single excitation system.

Turning to FIG. 8C, a schematic representation of part 550 of theoptical unit is seen, employing multi-wavelength excitation of FIG. 8Aand the dichroic filter of FIG. 5B, in accordance with an embodiment ofthe present invention. Part 550 may, in some cases, replace subsystem475 (FIG. 7B).

Table 1 shows representative values for representative components foruse in the present invention.

Laser Wavelength 405 nm 488 nm Laser Power  50 mW  20 mW or 50 mWSensing Spectral Range 200 nm 200 nm Spectral Resolution  25 nm  25 nmNumber of Detectors  8  8 Collecting Optics Microscope ObjectiveMicroscope Objective N.A. > 0.4, N.A. > 0.4, W.D. ≈ 6 mm W.D. ≈ 6 mmDetector Type S.S. PMT 8 ch S.S. PMT 8 ch

While much of the previous discussion has focused on the opticalelements of some embodiments of the present invention, one of the keycomponents of the diagnostic system herewith presented is a disposablesample cartridge.

Reference is now made to FIG. 9A, which is a schematic view of asampling cartridge 110 of FIG. 1A, in accordance with an embodiment ofthe present invention. The cartridge 650 includes a pre-analyticalcomponent 652 into which a sample (not shown) may be introduced.

The sample will generally be blood, either whole or a component (serum,etc.) thereof. Other liquid samples may additionally or alternatively beemployed. In the pre-analytical component 652, the sample is allowed tointeract with chemicals pre-packaged into component 652. The interactionmay be either passive or include active mixing. The chemicals includedin the analytical component 652 may be either wet or dry, and generallyinclude antibodies associated with fluorescent probes. Antibodies arepre-selected for their ability to bind with predetermined biologicalmarkers or the like. In a typical experiment, a predetermined volume(generally less than 50 microliters) of blood is introduced into thepre-analytical component 652 of a disposable cartridge 650. The sampleis actively mixed with chemical reagents present in the pre-analyticalcomponent 652 for a predetermined period of time, generally less thanten minutes. The sample is then moved through a capillary region 653 bymeans to be discussed, where it is exposed to a light beam 642 deliveredfrom an objective 638. Direction of sample flow is as shown by the arrowin the capillary region 653.

The capillary region 653 is designed to allow flow of particles in asingle-file past the light beam 642. Such an arrangement allows both forcounting the number of particles as well as individual interrogation ofparticles to determine the presence of biological markers (via theirassociated fluorescent tags) on each particle. Such a physicalarrangement allows for detection of one or more biological markers(independent of particle-specific properties such as size, shape, andnumber) on each particle.

Finally, there is a collection component 654 which receives sample afterexposure to light beam 642. This is a waste region and allows for acompletely self-contained disposable for sample preparation, analysisand waste collection. It is noted that the disposable cartridge may beof any relevant shape and is shown as it is in FIG. 6 for ease ofunderstanding of its components and functionality.

As mentioned above, the sample, after pre-analytical treatment to allowfor binding of fluorescent tag to cells/particles, must flow under alight beam 642, produced by an optical unit (not shown). The flow isgenerally “single file” so as to allow for accurate determination ofcell-specific markers on each analyzed cell. Methods to induce flowinclude but are not limited to electrical stimulation, chemicalinduction, and vacuum pull. In an electrical stimulation system, chargeis applied across the capillary region 653 so as to induce chargedparticles to move from the pre-analytical component 652 towards thecollection component 654. The charge could be supplied by the cytometerin which the disposable cartridge 650 is placed or from an externalsource.

Alternatively, the capillary region may include chemical features(hydrophilic/hydrophobic; positive/negative charge) to encourage sampleto move from left to right as shown in FIG. 9A. Alternatively, a vacuumfrom the collection component 654 could be applied to pull sample fromthe pre-analytical component 652 through the capillary region 653. Othermethods may be employed to get liquid sample to move underneath thelight beam 642 for analysis.

As described herein, the optics and sample handling have been handledseparately. Such an arrangement is not mandatory, as some of the opticalfeatures needed for proper sample analysis may be included in adisposable cartridge.

Reference is now made to FIG. 9B, which shows a schematic view ofdisposable cartridge 800 in flow-cytometer device, such as system 100 inaccordance with an embodiment of the present invention. Attention iscurrently turned to FIG. 9B which shows an expanded view of a capillaryregion 853.

In the capillary region 853, particles flow in the direction assuggested by the arrow 880. Particles 890 flow past an objective 838that shines light 842 through the capillary 853. Flow restrictionelements 894 may be present in the capillary region 853 so as toencourage particles 890 to move past the light 842 in a nearlysingle-file manner. Passage of multiple particles together may beresolved through processing software.

A molecular marker 895 on a particle 890 may be illuminated by light 842and its fluorescence will be captured by a proximate photomultipliertube 899. The photomultiplier tube 899 may distinguish the wavelength ofthe fluorescence and thus which biological marker 895 is present onparticle 890. Thus, the systems of the present invention may determinewhich biological markers are present on particles 890, which aredetected in the systems of the present invention. A photomultiplier tube899 may have a plurality of tubes or an array of elements for finewavelength discrimination and alternatively may be replaced with film,CCD or other appropriate light-receiving reader unit. It should beunderstood that FIG. 9B shows one embodiment of the configuration ofsystem 101 (FIG. 1) in a transmissive configuration, wherein detector(photomultiplier tube 899) is disposed on an opposing side of thecartridge 800 to objective 838.

The systems of the present invention comprise controller software whichare adapted to run a diagnostic process. It is understood that thecontroller software may be an integral part of the flow-cytometer oralternatively be installed on an associated computing device 122 (FIG.1B), which may include, but not be limited to, a laptop computer, iPod,iPad, cell phone or mainframe computer.

Reference is now made to FIG. 10, which is a simplified flowchart 1000of a method for rapid determination of a medical condition, inaccordance with an embodiment of the present invention. It is to beunderstood that the method described herein depicts one non-limitingembodiment of the present invention for determining the health state ofa patient. Further embodiments are also construed to be part of thepresent invention.

In a body fluid provision step 1002, a body fluid, such as blood, urine,serum or plasma is provided from a human or animal patient. Typically,the sample is fresh, but may also be a stored, refrigerated orfrozen-thawed sample. The fluid is typically liquid and at a temperatureof 4-37° C.

In a body fluid introduction step 1004, part or all of the body fluidsample 6051 (FIG. 6) is introduced into disposable cartridge (110, FIG.1A).

In a reacting step 1006, the fluid sample is reacted with at least onereactant in the cartridge forming a treated sample. According to someembodiments, this step is performed in pre-analytical sample processingsection 6054 (FIG. 6) as described in detail hereinabove.

In an impinging step 1008, radiation is impinged on the treated sample,such as, but not limited to, in a sample excitation/interaction section6056, thereby generating a plurality of spectrally distinct signals inthe direction of optics unit 142 (FIG. 1C, see description hereinabove).

In a spectral emissions detection step 1010, a plurality of spectrallydistinct signals is detected by multiple emission detector 454 (FIG.7A). The detector outputs data.

Thereafter, in a data processing step 1012, the outputted data isprocessed by signal processor 6036 (FIG. 6) and/or by computer 122 (FIG.1C) to provide an output indicative of a medical condition.

FIG. 11 is a three-dimensional graph showing the optical output overtime of reference beads (RM) relative to a sample from a human patient(PMN), in accordance with an embodiment of the present invention.

FIG. 11 shows a three-dimensional graph showing the optical output overtime of reference beads (RM) relative to a sample from a human patient(PMN), in accordance with an embodiment of the present invention. Theemission amplitude in the six bands, 500-525 nm, 525-550 nm, 550-575 nm,575-600 nm, 600-625 nm and 625 to 650 nm is displayed in the graph foreach sample time. Different fluorophores have different emissionspectra. It can be appreciated that both spectral content or shape andamplitude at individual wavelengths are significantly different forneutrophils stained with Acridine Orange (AO) and reference beads (RM)containing a bright broad spectrum fluorophore. The peak of the AOemission is in the 525-550 nm band, while that of RM is in the 500-525run band and is of a significantly greater amplitude than AO in anyband.

FIGS. 12A-12C show graphs of optical outputs over time of the referencebeads and the sample from a human patient, in accordance with anembodiment of the present invention.

Turning to FIGS. 12A-12C, there can be seen graphs of optical outputsover time of the reference beads and the sample from a human patient, inaccordance with an embodiment of the present invention. In thesetwo-dimensional figures, the traces from each of the bands are overlaidon the same graph. FIG. 12A shows the boxed pulses from neutrophils inFIG. 12B. It is clear from these graphs that the amplitude in the525-550 nm channel exceeds the amplitude in the 500-525 nm channel,which is the characteristic of AO. FIG. 12C shows a comparison of the AOstained neutrophil emission spectrum to that of the RM emissionspectrum. The relative amplitude of the spectrum in the 500-525 nm bandto that of the amplitude in the 525-550 nm band clearly distinguishesthe two fluorophores. In addition, the maximum amplitude of the RMemission is significantly greater than that of AO.

The systems of the present invention, as described and shown hereinprovide uses, such as, but not limited to, at least one of the fourfollowing scenarios:

-   -   a) When multiple pieces of information, such as biological        markers and white cell state are required in order to make an        accurate diagnostic determination;    -   b) When multiple sequential measurements must be made in order        to determine the position of a patient on an illness curve;    -   c) When white cell and similar data are needed quickly and in a        POC environment; and    -   d) When fluorescent signals overlap in wavelength and there is        need to determine relative contribution of each signal for a        given wavelength range.

The instant invention includes software and algorithms for proper dataanalysis and conversion of raw fluorescence data into actualconcentrations of relative biological markers.

FIG. 13A is an outer side view of a cartridge assembly 1300, inaccordance with an embodiment of the present invention and FIG. 13Bshows an inner side view 1350 of a cartridge assembly 1300, inaccordance with an embodiment of the present invention.

FIG. 14A-14O show a sequence of process events in a cartridge assembly,in accordance with an embodiment of the present invention;

FIG. 14A-14O are a sequential set of schematic drawings of the operationof a system 101 (FIG. 1A) for detecting a biological condition, inaccordance with an embodiment of the present invention.

In FIG. 14A, a blood sample 1401 enters a specimen receiving element1418 and fills a chamber 1404.

In FIG. 14B, a blister 1420 comprising a treatment composition 120(FIG. 1) is pressed and an antibody cocktail is mixed with 10microliters of the blood sample.

In FIG. 14C, a mixing bellows 1415 is pressed and this effects mixing ofthe antibody cocktail and the 10 microliters of the blood sample in afirst mixing chamber 1412 to form a first mixture 1403.

In FIG. 14D, the bellows is released and mixture 1403 is siphoned alonga tortuous channel 1413 and into a second mixing chamber 1411. Uponrelease of the bellows, the first mixture returns from the second mixingchamber, back along the tortuous channel to the first mixing chamber.Every time the bellows is pressed the mixture moves towards the secondchamber and every time it is released, it returns, wholly or in part tothe first chamber. This mixing may be performed multiple times.

In FIGS. 14E-14G, a second composition blister 1422 is pressed,releasing a second composition 122 (FIG. 1), such as a lysis compositionthereby forming a second mixture 1405. The second mixture is mixed bypressing of bellows 1415, the second mixture returns from the secondmixing chamber, back along tortuous channel 1413 to the first mixingchamber. Every time the bellows is pressed the mixture moves towards thesecond chamber 1411 and every time it is released, it returns, wholly orin part to the first chamber 1412. This mixing may be performed multipletimes.

In FIGS. 14H-14J, a third blister 1424 is released comprising a thirdcomposition 124 (FIG. 1), such as a control reference, into the secondmixing chamber, thereby forming a third composition 1407. The thirdmixture is mixed by pressing of bellows 1415, the third mixture returnsfrom the second mixing chamber, back along tortuous channel 1413 to thefirst mixing chamber. Every time the bellows is pressed the mixturemoves towards the second chamber 1411 and every time it is released, itreturns, wholly or in part to the first chamber 1412. This mixing may beperformed multiple times.

In FIGS. 14J-14M, a reading bellows 1417 is pressed, which forces someof the third composition towards a reading cuvette 1430.

In FIGS. 14N-140, particles 1460 from the third composition flow fromthe cuvette 1430 along a reading channel 1452 to a reading region 1450.The cells pass through the reading region and are excited by one or morelasers 1462, 1463. At least one excitation laser beam 1464 impinges oncell 1460 and an emission beam 1466 is detected by a detector 1470. Inone example, this is cell emission fluorescence and detector 1470 is aspectrometer.

FIG. 15 is a schematic illustration of a micro flow spectrometerreading, in accordance with an embodiment of the present invention;

An individual cell 1505 flows through a detection region 1510 in amicrofluidic channel (seen as 1452, FIG. 14M). Additionally, taggedcells 1520 labeled with antibodies conjugated with multiple wavelengthfluorescent tags flow through the detection region. A diode laser 1530impinges a ray/beam 1510 onto the cells and tagged cells. The cells andtagged cells emit different emission spectra (not shown). An opticalgrating 1540 disperses emission spectra via a grating 1540 into itsconstituent wavelengths 1550.

A photomultiplier tube (PMT) array 1560 or avalanche diode array detectsfluorescence at 8 different spatial locations corresponding to 8spectral regions.

FIG. 16 is a flow chart of a method for optical processing 1600, inaccordance with an embodiment of the present invention.

In a forming laser step 1602, a laser excitation beam shape is formed.

The excitation beam is reflected from a dichroic mirror 504 (FIG. 8A, or472 FIG. 7B) and through objective 476 (FIG. 7B) onto a reading channel1452 (FIG. 14M), in a reflecting step 1604.

In a forward scatter measuring step 1606, the forward scatter fromparticles 1460 (FIG. 14N) in the reading channel is measured to detectevents.

Thereafter, in a passing step 1608, particle fluorescent emission isallowed to pass through a dichroic mirror and be reflected from abeamsplitter 468 into a detection path.

In an imaging step 1610, parts of the beam emission, which are notreflected are passed through the beamsplitter onto an image sensor, suchas silicon detector 462 (FIG. 7B).

In parallel to step 1610, the reflected part of the beam is filtered ina beam filtering step 1612 in the detection path to allow onlywavelengths above an excitation wavelength to pass through a filter.

In a focusing step 1614, the filtered beam from step 1612 is focusedonto a pinhole or slit to select a reading zone region to be analyzed.

Thereafter, in a dispersing step 1616, the dispersed pinhole or slit isdispersed and imaged onto a multi-element electrooptical detector (6034,FIG. 6).

FIGS. 17A-17B are schematic illustrations of steps of use of a graphicaluser interface, in accordance with an embodiment of the presentinvention;

Upon powering up the unit a first screen 1702 appears with a messagenotifying the user that the system is performing a self-check along witha countdown indicator 1703. Once the self-check is complete, an assayselection screen 1704 appears. The user touches the button correspondingto the assay to be performed. The next screen 1706 is used to enter thepatient identification. This may be done by touching the numerals of thetouchpad 1709 or by scanning a barcode. Once the entry is complete, theuser touches the forward button 1707 and a screen requesting the user toenter the cartridge 1708 appears. Once the user inserts the cartridgethe system checks to ensure that the cartridge identified by its barcodelabel corresponds to the selected assay and begins the processing. Whileprocessing, a screen 1710 is displayed showing the processing progressand the time remaining. Once the pre-analytical and analyticalprocessing is completed the results are displayed on a screen 1712 withan indication of where the results lie in the range of possible results1713. After the user touches a “proceed to next screen indicator” 1711 ascreen instructing the user to remove the cartridge 1714 appears. Theuser has the option of repeating this test with another sample bypressing the repeat icon 1715 or displaying the most recent results on ascreen 1716.

Reference is now made to FIG. 18, which is a simplified illustration ofa method for a disposable cartridge 1850 of system 101 of FIG. 1A forrapid determination of a medical condition, in accordance with anembodiment of the present invention.

When practicing the method of disposable cartridge 1850 a bodily fluid,such as, but not limited to, blood, urine, serum or plasma istransferred from the donor to the cartridge 1851. The disposablecartridge method includes multiple steps to effect the analysis anddiagnosis 1852, 1854, 1856 and 1858. In step 1852 a body fluidaspiration step, receives the body fluid directly or indirectly from thepatient (or animal) and transfers the body fluid to a reservoir.

The disposable cartridge method 1850 utilizes fluid conveying means,such as, but not limited to, air pressure, liquid pressure, mechanicalmeans and combinations thereof to move fluids. Body fluid aspirationstep 1852 is adapted to convey a predetermined quantity of the bodyfluid (a body fluid sample 1851) for a pre-analytical sample processingstep 1854.

In pre-analytical sample processing 1854, at least one preparatory stepis performed on the body fluid such as, but not limited to:

-   -   i) incubation with at least one antibody;    -   j) incubation with at least one antigen;    -   k) staining of at least one cell type in the body fluid;    -   l) enzymatic lysing of at least one cell type of the body fluid;    -   m) osmotic lysing of at least one cell type of the body fluid;    -   n) heating or cooling at least part of the bodily fluid;    -   o) addition of reference material to the bodily fluid; and    -   p) chemical reaction with at least one element of the body        fluid.

The pre-treated sample of bodily fluid is then transferred (1855) afterpre-analytical sample processing step 1854 to a sampleexcitation/interaction step 1856. This pre-treated sample transfer forexcitation/interaction 1856 may be performed continuously or in a batchmode.

Part of sample excitation/interaction 1856 is to position the sample tosit in the light path of an excitation illumination. The excitationillumination passes radiation, such as coherent or incoherent radiationin or outside the visible range into the pre-treated sample. Resultantemission or emissions from the pre-treated sample is detected 1834, andprocessed 1836 to produce a report 1812 summarizing the analysis anddiagnosis.

Multi-spectral emission detection 1834 receives the emission from thepre-treated sample in multiple spectral bands. In some cases these bandsare non-overlapping bands. Multi-spectral emission detection 1834 isadapted to pass data representing the spectral bands to multi-spectralfluorescence signal processing 1836.

Multi-spectral fluorescence signal processing 1836 may comprise two ormore sub-elements (not shown) including:

-   -   a) a photon counting analysis;    -   b) other detecting analysis elements (not shown) for measuring        other optical outputs of multi-spectral emission detection 1834.

The method further comprises a spent sample disposal method 1858, forreceiving a sample from the sample excitation/interaction processing.

The method further comprises computer program 1810, the computer programis adapted to receive data related to the plurality of spectrallydistinct signals and a processor, adapted to process said data and tooutput at least one output related to said medical condition. One typeof output provided is a visual output which is outputted onto a screen1812 of the computer.

FIG. 19A is a simplified flow chart of a method 600 for differentiatingbetween different particles, in accordance with an embodiment of thepresent invention.

The input to the processing is a time series from each of the channelsin the eight channel photomultiplier array 601. In addition, data frommultiple scatter channels 609 is introduced. Each fluorescent timeseries and scatter time series may be processed individually employingrespective spectral cross-correlation algorithm 606 and scatteralgorithm 607 to smooth it and minimize noise. Two possible processingmethods are boxcar averaging algorithm 602 and matched filteringalgorithm 604. In addition, groups of individual channels may becorrelated to yield a multiple spectral crosscorrelations 606. One ormore of these derived time series may be used to determine eventlocations.

Once an event is located in the eight channel time series thecomposition of that event in terms of known fluorophore signatures isdetermined using a minimum mean square error fit 610. The event is nowdescribed in terms of its composition of known fluors. Each event thusdescribed is stored in an event store, i.e. memory, together with thedata from the eight time series for that event and its description 612.Based on the fluor composition for each event in the data store, it ispossible to determine the type of particle. For example, a neutrophil616 is characterized by the single fluor attached to the CD64 antibodyshown in FIG. 5 as W1. Thus events that are preponderantly characterizedby the single fluor attached to the CD64 antibody are identified asneutrophils.

Similarly, monocytes 618 are characterized by fluors W1 and W2 so thatan event with both of these fluor signatures is identified as amonocyte. Similarly, a bead 620 is characterized by an event that hasfluors W1 and W3. Lymphocytes 622 do not express significantfluorescence but are identified by their scatter as events. Events thatdo not match any of the known combinations of the fluorophores areidentified as rejects 626.

Given the population of identified events, the median intensity of theneutrophil population and the median intensity of the bead populationare determined. The ratio of the neutrophil median to the bead median isthe desired Leuko64 index. The positive control value is determined asthe median intensity of the CD64 fluorophore bound to monocytes dividedby the median intensity of the same fluorophore on the bead population.The negative control value is determined by the median intensity of theCD64 fluorophore bound to lymphocytes. These are the key steps inperforming the Leuko64 assay.

FIG. 19B is a flow chart of an algorithm for biological detection 1900,in accordance with an embodiment of the present invention;

FIG. 19 B shows schematically that the CD4/CD8 assay is performed bydetermining a particle type for each event in the event store 1912. Onemethod to accomplish this particle selection is to use K meansclustering to determine data clusters in the event store based on thesignatures Alexa 488, PE 488N and PEAF 488N as shown in FIG. 25. Basedon these three signatures events with large values of PE 488N areclassified as CD4 positive lymphocytes 1938 since the phycoerythrin (PE)fluor is attached to the CD4 antibody. Events with large values of Alexa488 are classified as CD8 positive lymphocytes 1940 since the Alexa 488fluor is attached to this CD8 antibody. Events with large values of PEAF488N are classified as lymphocytes since this fluor is attached to theCD3 antibody which is expressed by lymphocytes to the exclusion of otherWBC. The group 1942 has large values of PEAF 488N but small values of PE488N and Alexa 488 which corresponds to lymphocytes not expressingeither CD4 or CD8. Finally, non-lymphocytes WBC 1936 may be determinedby a pan WBC antibody for those events not expressing CD3, and rejectsas those events not expressing the pan WBC antibody.

FIGS. 20A-20B shows bandwidth leveled and smoothed arrays, in accordancewith an embodiment of the present invention.

FIGS. 20A and 20B show the typical response of the system to fluorescentbeads with an F488 signature. The response in 25 nm bands from 500 nm to700 nm are respectively 2010, 2020, 2030, 2040, 2050, 2060, 2070, and2080. The traces represent the outputs from the eight channelfluorescent detector with noise, characterized as the median tracevalue, subtracted. The large signals above the background level are theraw signal smoothed by a box car averager of length 10. The peak valuefor the F488 signature occurs in the range 525 to 549 nm, 2020. The nexthighest value occurs in the range 500 to 524 nm, 2010, with decreasingamplitudes in each 25 nm band, 2030, 2040, 2050, 2060, 2070, and 2080.

FIGS. 21A-21B are schematics for solving a fluor decomposition of anobserved signal, in accordance with an embodiment of the presentinvention.

FIG. 21A is the Matlab function used to solve the matrix equation Ax=bfor the signature value vector or vectors b corresponding to theobserved eight channel emission values x. The \ function in Matlab isused to solve for x using the Matlab expression x=A \b.

FIG. 21 B is a table of fluor signatures use as the matrix A describedin FIG. 21A.

FIGS. 22A-22B is a graphical comparison of system performance with FITCbeads with MESF detection versus FACS, in accordance with an embodimentof the present invention.

FIG. 22A shows a comparison of the linearity of the instant inventionwith that of a Becton Dickinson FACS flow cytometer. The tabulatedmedian values for the FITC MESF beads are shown in column 2211 in table2210. The median fluorescent intensity levels (in arbitrary units) forthe FACS flow cytometer are shown in column 2212, while those for theinstant invention are shown in column 2213. Column 2214 shows the numberof events on which the median value is based for the instant invention.The linearity plot for the full range of values for the instantinvention is shown in 2220 while that for the FACS flow cytometer isshown in 2230. Also shown in each of these figures is the best fit linethrough the points along with the square of the correlation value, R2.Comparison of these plots shows comparable performance of the instantinvention and the FACS flow cytometer.

FIG. 22B shows a comparison of the linearity of the instant invention2240 with that of the FACS flow cytometer 2250 over the range restrictedto the first four smallest data points. Again, comparable performance isdemonstrated.

FIGS. 23A-23B show graphical displays of linearity of system performancewith Alexa 488 MESF, in accordance with an embodiment of the presentinvention.

FIGS. 23A and 23B shows the linearity performance of the instantinvention for the Alexa Fluor 488 MESF bead series when the system isrun both add fast speed 2310 and flow speed 2330. In this case themeasure of performance is the F488 signature normalized to the length ofthe event. This normalized signature is designated F488N. The tabularlistings 2320 and 2340 summarize the statistics for the regression linefit.

FIG. 24 is a three-dimensional graph showing the optical output overtime of a CD4-CD8 assay, in accordance with an embodiment of the presentinvention.

FIG. 24 is a surface plot showing the relative amplitude of eventemission in each of the detectors for a thirty second interval. Thescale running from left to right 2440 is in 10 μs intervals. The scalerunning from right to left 2450 and numbered one through eight are thedetector elements. Eight corresponds to waveband 1, seven corresponds towaveband 2, and finally one corresponds to waveband 8. An example of CD4events tagged with phycoerythrin shown in 2510 in FIG. 25 is the Trace2430. An example of CD8 events tagged with Alexa Fluor 488 shown in 2520in FIG. 25 is the trace 2410. Finally an example of non-CD4 non-CD8lymphocytes tagged only with Alexa Fluor 610 shown in the group 2530 inFIG. 25 is the trace 2420.

FIG. 25 is a graphical display showing a cluster analysis of a CD4-CD8assay, in accordance with an embodiment of the present invention;

FIG. 25 is the scatterplot matrix showing the result of applying K meansclustering to the signatures Alexa 488N, PE488N and PEAF488N. Themeaning of each of the clusters 2510, 2520 and 2530 is described in thedescription of FIG. 19 B.

FIGS. 26-27 are graphical displays showing cluster separations of thecluster analysis of FIG. 19A, in accordance with an embodiment of thepresent invention.

FIG. 26 is a scatterplot matrix showing four-color separation of theneutrophil, monocyte, lymphocyte and reference bead populations requiredto effect a CD64 assay. The leftmost column 2710 shows the complete4-color separation. The top frame 2720 shows separation of NE & LY fromMO and BEADS based on Waveband2 (Alexa488) and separation of MO fromBEADS based on Waveband4 (PE).

The middle frame 2730 shows separation of LY from NE based on Waveband6(A610).

The bottom frame 2740 shows separation of beads from cells based onWaveband8 (Starfire Red).

Since the separation is based on individual narrow bands (notsignatures) 45 degree clusters 2750, 2760, 2770 show emission presencein two bands, which in each case is as expected as can be seen from theemission signatures in the table below.

FIG. 28 is a comparison table of different array options, in accordancewith an embodiment of the present invention.

FIG. 28 is a tabular listing of photomultiplier arrays produced byHamamatsu Corporation. The H95308 channel array is the one used in thecurrent implementation of the extant invention. One skilled in the artwill appreciate that finer resolution or greater extent of the spectralsampling can be achieved by using either the 16 or 32 channel arrayproducts.

FIG. 29A is a flowchart of a specific implementation of an algorithm1300 for selecting groups of data from a scatterplot, in accordance withan embodiment of the present invention;

The algorithm in FIG. 29A is a specific implementation of the generalalgorithm in FIG. 29B to select each of the groups 3010, 3020, 3030 and3040 (FIG. 30) and determine specific parameter values in each of thegroups.

In a first ordering signature step 1304 the Star Fire Red (SFR)signature is used to order (from smallest SFR signature to largest) theentire dataset of waveband and signature values 1302.

In a second step 1320, an analysis of a histogram of an SFR signaturevalues as shown in FIG. 14A to select the group 1210. This is a smallgroup 1404 at the upper end of group 1402 in the histogram 1400 in FIG.31A. The next step is to remove this group from the overall dataset asshown in FIG. 29A Step 1322. The removed group is the bead dataset 1324.

A dataset of Waveband and Signature values with bead dataset removed1340 is then manipulated as follows. In an ordering step 1342, the datais organized according to its PE (phycoerythrin) signature from smallestto largest PE (phycoerythrin) signature.

In an analyzing PE histogram set step, 1344, the data is manipulated tofind a group corresponding to monocytes.

In an extracting monocytes dataset step 1346, a monocyte dataset ofwaveband and signature values 1348 is extracted. A dataset of wavebandand signature values with beads and monocytes removed 1360 is thenfurther processed as follows. Set 1360 is organized according to itsPEAF (full name PEAF®488) (see above for beads and PE) signature in anorder according to PEAF signature ordering step 1362.

In an analyzing PEAF histogram to find a group corresponding tolymphocytes step 1364, set 1360 is analyzed to determine if any of thedata have behavior corresponding to lymphocytes.

In an extraction step 1366, a lymphocyte dataset of waveband andsignature values 1368 is extracted from set 1360 and the remainingdataset is a dataset of waveband and signature values with bead,monocytes and lymphocytes removed 1380.

In an order by Diodel signature step 1382, dataset 1380 is analyzedaccording to a Diodel signature (see above). Dataset 1380 is thenanalyzed in an analyzing step 1384 to find a group of data havingproperties of neutrophils.

In an extracting step 1386, a group of data having properties ofnon-neutrophils 1388 is removed. A remaining group 1391 (assumed to beneutrophils) is used in a computing step 1392 to compute desired metricfrom the group parameters.

Reference is now made to FIG. 29B, which is a flowchart of a generalimplementation of an algorithm 1350 for selecting groups of data from ascatterplot, in accordance with an embodiment of the present invention.

In a first ordering signature step 1305 a first signature is used toorder the dataset of waveband and signature values 1303.

In a second step 1321, an analysis of a histogram of a 1st signaturevalues to find the group corresponding to 1^(st) signature 1325, asexemplified in FIG. 31A to select the group 3010. This is a small group1404 at the upper end of group 1402 in the histogram 1400 in FIG. 31A.It should be noted that this is but one way to select the group andother methods employing additional data set values in combination may beused. The next step is to remove this group from the overall dataset asshown in FIG. 31B Step 1323. A removed group is a 1st signature dataset1325.

A dataset of Waveband and Signature values with 1st dataset removed 1341is then manipulated as follows. In an ordering step 1343, the data isorganized according to its 2nd signature.

In an analyzing 2^(nd) signature histogram set step, 1345, the data ismanipulated to find a group corresponding to the 2^(nd) signature.

In an extracting 2^(nd) signature dataset step 1347, a 2^(nd) signaturedataset of waveband and signature values 1349 is extracted. A dataset ofwaveband and signature values with 1^(st) and 2^(nd) signatures groupsremoved 1361 is then further processed as follows. Set 1361 is organizedaccording to its signature in an order according to i^(th) signatureordering step 1363.

In an analyzing i^(th) histogram to find a group corresponding to i^(th)signature step 1365, set 1361 is analyzed to determine if any of thedata have behavior corresponding to the i^(th) signature.

In an i^(th) signature extraction step 1367, an i^(th) signature datasetof waveband and signature values 1369 is extracted from set 1381 and theremaining dataset is a dataset of waveband and signature values with1^(st) 2^(nd) and i^(th) signature groups removed 1381.

In an order by N^(th) signature step 1383, dataset 1381 is analyzedaccording to an N^(th) signature. Dataset 1381 is then analyzed in ananalyzing step 1385 to find a group of data having properties of nothaving Nth signature properties.

In an extracting step 1387, a group of data having properties of non-Nthsignatures 1397 is removed. A remaining group 1395 (assumed to be Nthgroup) is used in a computing step 1393 to compute desired metric fromthe group parameters.

FIG. 31A is a histogram 1400 of data of Starfire Red (SFR) signaturevalues, in accordance with an embodiment of the present invention.

FIG. 31B shows a plot 1450 of a polynomial 1452 and first derivativethereof 1456 and second derivative thereof 1458 of histogram 1400 shownin FIG. 31A, in accordance with an embodiment of the present invention.

Referring to FIG. 31B, the method of determining an upper group 1404 inFIG. 31A is as follows. A polynomial 1452 of sufficient degree is fittedto the histogram data 1454 (as shown in FIG. 13A, set 1324) is shown inFIG. 14B. The first derivative 1456 and the second derivative 1458 ofthis polynomial are computed. A plurality of zeros 1460 of the firstderivative are indicated by the square boxes along the zero line. Apoint where the polynomial is both maximum and has a zero derivative1462 is indicated by the box with an X in it. This point in thehistogram corresponds to the peak of the large group 1402 (FIG. 31A). Anext zero 1464 of the derivative of the polynomial corresponds to theend of the large group in the histogram. All points in the histogramabove this value are in the small group. Since the dataset has beenordered from smallest to largest based on the value of SFR488, and thehistogram horizontal axis is also ordered from smallest to largest valueof SFR488 the point at which the large group ends is the value of SFR488above which records in the SFR488 ordered dataset are to be removed andidentified as the bead dataset 1324 of waveband and signature values asindicated in FIG. 13A.

FIG. 32A is a histogram 1500 of data of PE488 signature values, inaccordance with an embodiment of the present invention.

FIG. 32B shows a polynomial fitted to the histogram in FIG. 32A as wellas a corresponding first derivative 1556 and a second derivative 1558,in accordance with an embodiment of the present invention.

The records remaining in the dataset are now reordered using the PE488signature from smallest to largest. Histogram 1500 of the PE488signature values 1502 is shown in FIG. 32A. Again in this case, there isa small group 1504 to the right of the large group 1502 whichcorresponds to the desired monocyte population. FIG. 32B shows thepolynomial 1552 fitted to data 1554 of histogram 1500 in FIG. 32A aswell as the corresponding first and second derivatives. The upper group1504 is determined in the same way as the upper group of the SFR488histogram as was described previously. It should be noted that while inboth of these cases only a one dimensional histogram was analyzed andused as the basis for selecting the desired population, multiple fieldsfrom each record in the dataset may be used to effect a group selection.

As noted in FIG. 31A, the monocyte group 1504 is removed from thedataset which now contains primarily lymphocytes, neutrophils and otherparticles such as unlysed erythrocytes and other debris.

FIG. 33A is a histogram 1600 of data 1602 of PEAF488 signature values,in accordance with an embodiment of the present invention.

FIG. 33B shows a polynomial 1652 fitted to histogram data 1654 from FIG.33A as well as a corresponding first derivative 1656 and a secondderivative 1658, in accordance with an embodiment of the presentinvention.

The records remaining in the dataset are now reordered using a PEAF488signature corresponding to lymphocytes. A histogram 1600 of the PEAF488signature is shown in FIG. 33A and the corresponding polynomial fit withits first and second derivatives are shown in FIG. 33B. The processoutlined above is applied in this case as well to identify and remove asmall group 1604 appearing at an upper end of the histogram, from alarge group 1602. The lymphocyte group is now removed as shown in FIG.29A leaving a dataset 1380 which now contains primarily neutrophils andother particles such as unlysed erythrocytes and other debris.

While neutrophils 1391 are tagged with a fluorophore with an F488signature, other particles appear to express this signature because ofthe unbound fluorophore in solution. The other particles, however, aresmaller than neutrophils, which now comprise the group with the largestforward scatter as measured by a Diodel (forward scatter detector)channel. A histogram of the Diodel channel is shown in FIG. 34A.

FIG. 34A is a histogram 1700 of data of Diode 1 channel signaturevalues, in accordance with an embodiment of the present invention.

FIG. 34B shows a polynomial 1752 fitted to data 1754 from the histogramin FIG. 34A, as well as a corresponding first derivative 1756 and asecond derivative 1758, in accordance with an embodiment of the presentinvention.

As described above, an upper group 1704 (FIG. 34A) corresponding tolarger particles, which are the neutrophils is selected. This completesthe decomposition of the original dataset 1302 into the four distinctevent groups (1324, 1348, 1368, 1391) shown in FIG. 29A.

Within each group various parameters may be computed from the fields inthe dataset. An example is shown in the following table.

MEDWave- MEDWave- INDEX INDEX Observations NAM MEDUG MEDF488 band2band2N INDEX488 Waveband2 Waveband2N SFR488 166 978.72 3395.26 3062.00503.80 1.00 1.00 1.00 PE488 73 3851.88 5968.83 5843.50 723.66 1.76 1.911.44 PEAF488 332 1164.38 −4.36 37.00 4.63 0.00 0.01 0.01 F488 620 379.98379.98 361.00 37.92 0.11 0.12 0.08 Diodel 59 7027.00 −113.54 −73.00−6.81 −0.03 −0.02 −0.01

The observations column contains the name of the group. The NAM columnis the number of events in the group. The MEDUG column is the medianvalue of the signature for that group. For example in the SFR488 row themedian SFR488 signature value is 978.72. The MEDF488 column contains themedian value of the F488 signature for the specified group. TheMEDWaveband2 column contains the median value of the Waveband2 values inthe group. The MED Waveband2N column contains the median value of theWaveband2N values in the group. The INDEX488 column contains the ratioof the MEDF488 value for the group to that of the SFR488 group.Similarly, INDEXWaveband2 and INDEXWaveband2N are the ratios of theWaveband2 and Waveband2N medians for the group to that of the SFR488group.

Although, specific groups corresponding to leukocyte subsets and aspecific algorithm to compute a specific index based on these groups hasbeen illustrated, one skilled in the art can use this basic approachwhenever it is necessary to select groups from a dataset and computenumeric values based on parameters associated with these groups as shownin the general diagram of FIG. 29B.

Other suitable operations or sets of operations may be used inaccordance with some embodiments. Some operations or sets of operationsmay be repeated, for example, substantially continuously, for apre-defined number of iterations, or until one or more conditions aremet. In some embodiments, some operations may be performed in parallel,in sequence, or in other suitable orders of execution.

Discussions herein utilizing terms such as, for example, “processing,”“computing,” “calculating,” “determining,” “establishing”, “analyzing”,“checking”, or the like, may refer to operation(s) and/or process(es) ofa computer, a computing platform, a computing system, or otherelectronic computing device, that manipulate and/or transform datarepresented as physical (e.g., electronic) quantities within thecomputer's registers and/or memories into other data similarlyrepresented as physical quantities within the computer's registersand/or memories or other information storage medium that may storeinstructions to perform operations and/or processes.

Some embodiments may take the form of an entirely hardware embodiment,an entirely software embodiment, or an embodiment including bothhardware and software elements. Some embodiments may be implemented insoftware, which includes but is not limited to firmware, residentsoftware, microcode, or the like.

Some embodiments may utilize client/server architecture,publisher/subscriber architecture, fully centralized architecture,partially centralized architecture, fully distributed architecture,partially distributed architecture, scalable Peer to Peer (P2P)architecture, or other suitable architectures or combinations thereof.

Some embodiments may take the form of a computer program productaccessible from a computer-usable or computer-readable medium providingprogram code for use by or in connection with a computer or anyinstruction execution system. For example, a computer-usable orcomputer-readable medium may be or may include any apparatus that cancontain, store, communicate, propagate, or transport the program for useby or in connection with the instruction execution system, apparatus, ordevice.

In some embodiments, the medium may be or may include an electronic,magnetic, optical, electromagnetic, InfraRed (IR), or semiconductorsystem (or apparatus or device) or a propagation medium. Somedemonstrative examples of a computer-readable medium may include asemiconductor or solid state memory, magnetic tape, a removable computerdiskette, a Random Access Memory (RAM), a Read-Only Memory (ROM), arigid magnetic disk, an optical disk, or the like. Some demonstrativeexamples of optical disks include Compact Disk-Read-Only Memory(CD-ROM), Compact Disk-Read/Write (CD-R/W), DVD, or the like.

In some embodiments, a data processing system suitable for storingand/or executing program code may include at least one processor coupleddirectly or indirectly to memory elements, for example, through a systembus. The memory elements may include, for example, local memory employedduring actual execution of the program code, bulk storage, and cachememories which may provide temporary storage of at least some programcode in order to reduce the number of times code must be retrieved frombulk storage during execution.

In some embodiments, input/output or I/O devices (including but notlimited to keyboards, displays, pointing devices, etc.) may be coupledto the system either directly or through intervening I/O controllers. Insome embodiments, network adapters may be coupled to the system toenable the data processing system to become coupled to other dataprocessing systems or remote printers or storage devices, for example,through intervening private or public networks. In some embodiments,modems, cable modems and Ethernet cards are demonstrative examples oftypes of network adapters. Other suitable components may be used.

Some embodiments may be implemented by software, by hardware, or by anycombination of software and/or hardware as may be suitable for specificapplications or in accordance with specific design requirements. Someembodiments may include units and/or sub-units, which may be separate ofeach other or combined together, in whole or in part, and may beimplemented using specific, multi-purpose or general processors orcontrollers. Some embodiments may include buffers, registers, stacks,storage units and/or memory units, for temporary or long-term storage ofdata or in order to facilitate the operation of particularimplementations.

Some embodiments may be implemented, for example, using amachine-readable medium or article which may store an instruction or aset of instructions that, if executed by a machine, cause the machine toperform a method and/or operations described herein. Such machine mayinclude, for example, any suitable processing platform, computingplatform, computing device, processing device, electronic device,electronic system, computing system, processing system, computer,processor, or the like, and may be implemented using any suitablecombination of hardware and/or software. The machine-readable medium orarticle may include, for example, any suitable type of memory unit,memory device, memory article, memory medium, storage device, storagearticle, storage medium and/or storage unit; for example, memory,removable or non-removable media, erasable or non-erasable media,writeable or re-writeable media, digital or analog media, hard diskdrive, floppy disk, Compact Disk Read Only Memory (CD-ROM), Compact DiskRecordable (CD-R), Compact Disk Re-Writeable (CD-RW), optical disk,magnetic media, various types of Digital Versatile Disks (DVDs), a tape,a cassette, or the like. The instructions may include any suitable typeof code, for example, source code, compiled code, interpreted code,executable code, static code, dynamic code, or the like, and may beimplemented using any suitable high-level, low-level, object-oriented,visual, compiled and/or interpreted programming language, e.g., C, C++,Java, BASIC, Pascal, Fortran, Cobol, assembly language, machine code, orthe like.

Functions, operations, components and/or features described herein withreference to one or more embodiments, may be combined with, or may beutilized in combination with, one or more other functions, operations,components and/or features described herein with reference to one ormore other embodiments, or vice versa.

Any combination of one or more computer usable or computer readablemedium(s) may be utilized. The computer-usable or computer-readablemedium may be, for example but not limited to, an electronic, magnetic,optical, electromagnetic, infrared, or semiconductor system, apparatus,device, or propagation medium. More specific examples (a non-exhaustivelist) of the computer-readable medium would include the following: anelectrical connection having one or more wires, a portable computerdiskette, a hard disk, a random access memory (RAM), a read-only memory(ROM), an erasable programmable read-only memory (EPROM or Flashmemory), an optical fiber, a portable compact disc read-only memory(CDROM), an optical storage device, a transmission media such as thosesupporting the Internet or an intranet, or a magnetic storage device.Note that the computer-usable or computer-readable medium could even bepaper or another suitable medium upon which the program is printed, asthe program can be electronically captured, via, for instance, opticalscanning of the paper or other medium, then compiled, interpreted, orotherwise processed in a suitable manner, if necessary, and then storedin a computer memory. In the context of this document, a computer-usableor computer-readable medium may be any medium that can contain, store,communicate, propagate, or transport the program for use by or inconnection with the instruction execution system, apparatus, or device.The computer-usable medium may include a propagated data signal with thecomputer-usable program code embodied therewith, either in baseband oras part of a carrier wave. The computer usable program code may betransmitted using any appropriate medium, including but not limited towireless, wireline, optical fiber cable, RF, etc.

Computer program code for carrying out operations of the presentinvention may be written in any combination of one or more programminglanguages, including an object oriented programming language such asJava, Smalltalk, C++ or the like and conventional procedural programminglanguages, such as the “C” programming language or similar programminglanguages. The program code may execute entirely on the user's computer,partly on the user's computer, as a stand-alone software package, partlyon the user's computer and partly on a remote computer or entirely onthe remote computer or server. In the latter scenario, the remotecomputer may be connected to the user's computer through any type ofnetwork, including a local area network (LAN) or a wide area network(WAN), or the connection may be made to an external computer (forexample, through the Internet using an Internet Service Provider).

The present invention is described herein with reference to flow chartillustrations and/or block diagrams of methods, apparatus (systems) andcomputer program products according to embodiments of the invention. Itwill be understood that each block of the flow chart illustrationsand/or block diagrams, and combinations of blocks in the flow chartillustrations and/or block diagrams, can be implemented by computerprogram instructions. These computer program instructions may beprovided to a processor of a general purpose computer, special purposecomputer, or other programmable data processing apparatus to produce amachine, such that the instructions, which execute via the processor ofthe computer or other programmable data processing apparatus, createmeans for implementing the functions/acts specified in the flowchartand/or block diagram block or blocks.

These computer program instructions may also be stored in acomputer-readable medium that can direct a computer or otherprogrammable data processing apparatus to function in a particularmanner, such that the instructions stored in the computer-readablemedium produce an article of manufacture including instruction meanswhich implement the function/act specified in the flow charts and/orblock diagram block or blocks.

The computer program instructions may also be loaded onto a computer orother programmable data processing apparatus to cause a series ofoperational steps to be performed on the computer or other programmableapparatus to produce a computer implemented process such that theinstructions which execute on the computer or other programmableapparatus provide processes for implementing the functions/actsspecified in the flow charts and/or block diagram block or blocks.

The flow charts and block diagrams in the Figures illustrate thearchitecture, functionality, and operation of possible implementationsof systems, methods and computer program products according to variousembodiments of the present invention. In this regard, each block in theflow charts or block diagrams may represent a module, segment, orportion of code, which comprises one or more executable instructions forimplementing the specified logical function(s). It should also be notedthat, in some alternative implementations, the functions noted in theblock may occur out of the order noted in the figures. For example, twoblocks shown in succession may, in fact, be executed substantiallyconcurrently, or the blocks may sometimes be executed in the reverseorder, depending upon the functionality involved. It will also be notedthat each block of the block diagrams and/or flow chart illustrations,and combinations of blocks in the block diagrams and/or flow chartillustrations, can be implemented by special purpose hardware-basedsystems that perform the specified functions or acts, or combinations ofspecial purpose hardware and computer instructions.

Although the embodiments described above mainly address assessing testcoverage of software code that subsequently executes on a suitableprocessor, the methods and systems described herein can also be used forassessing test coverage of firmware code. The firmware code may bewritten in any suitable language, such as in C. In the context of thepresent patent application and in the claims, such code is also regardedas a sort of software code.

The cartridges of the present invention may be constructed andconfigured such that the treatment composition comprises proteinsattached to a surface, such as to beads. A plurality of beads or otherstructural elements with proteins attached to their surfaces can be madeby any one or more of the following methodologies:—

-   -   simple attachment such as by adsorption via electrostatic or        hydrophobic interactions with the surface, entrapment in        immobilized polymers, etc.    -   non-covalent or physical attachment;    -   covalent bonding of the protein to the bead surface    -   biological recognition (e. g., biotin/streptavidin).    -   requires two steps: a first layer is formed by silane chemistry        such that the surface presents a reactive group (e. g., epoxy,        amino, thiol, etc.), and a second layer (e. g., the protein to        be immobilized or a linker molecule) is covalently attached via        the immobilized reactive groups.    -   covalent attachment to functionalized polymer coatings on the        interior of the device or linkage to the free end of a        self-assembled monolayer (SAM) on a gold surface.

The reaction type may include any one or more of antigen-antibodybinding, sandwich (such as antibody-antigen-antibody), physicalentrapment, receptor-ligand, enzyme-substrate, protein-protein,aptamers, covalent bonding or biorecognition.

Table 2 shows some representative applications of apparatus 100 andmethods of the present invention.

TABLE 2 Applications of the apparatus and methods of this invention.Typical Prior This Relevant Art Laboratory invention Figures inTurnaround Turnaround Type of this time (TAT)- time Application Testinvention see references (TAT) References Application #1- Surface FIGS.1-2 4 hours 10 U.S. Pat. No. 8,116,984, CD64 Infection Marker and 3-5Dminutes Davis, BH et al., & Sepsis (2006) 1-Fetal Plasma FIGS. 1-2 4hours 10 Dziegiel et al. Hemoglobin Protein and 6-8D minutes (2006) Test2-Low Platelet Surface FIGS. 1-2 4 hours 10 Segal, H. C., et al. CountMarker and 3-5D minutes (2005): 3-Resolving Surface FIGS. 1-2 4 hours 10Guerti, K., et al. BLAST Flag for Marker and 3-5D minutes hematology Lab4-CD34 Stem Surface FIGS. 1-2 4 hours 10 Sutherland et al. Cell Markerand 3-5D minutes (1996) Enumeration Assay 5-Platelets Surface FIGS. 1-24 hours 10 Graff et al. (2002) Activation Marker and 3-5D minutesDivers, S. G., et al. Assay CD62 (2003) 6-D-dimer Plasma FIGS 1-2 4hours 10 Stein et al. (2004) (Bead based Protein and 6-8D minutesRylatt, D. B., et al. protein) (1983): 7- Surface FIGS. 1-2 4 hours 10Hillier et al. (1988) Chorioamnioitis Marker and 3-5D minutes CD648-CD20 Cell Surface FIGS. 1-2 4 hours 10 Rawstron et al. QuantitationMarker and 3-5D minutes (2001) (Therapy Cheson et al. Monitoring (1996)9-CD52 Cell Surface FIGS. 1-2 4 hours 10 Rawstron et al. quantitationMarker and 3-5D minutes (2001) (Therapy Monitoring) 10-CirculatingSurface FIGS. 1-2 4 hours 10 Cristofanilliet al. Tumor Cells Marker and3-5D minutes (2004 11-Reticulated Surface FIGS. 1-2 4 hours 10 Matic etal. (1998) Platelet Assay Marker and 3-5D minutes Ault et al (1993) Wanget al. (2002) 12-Bacteria 4 hours 10 Blajchman et al Detection inminutes (2005) platelet packs McDonald et al. (2005) 13-Platelet SurfaceFIGS. 1-2 4 hours 10 Michelson (1996) Associated Marker and 3-5D minutesAntibodies 14-Residual Surface FIGS. 1-2 4 hours 10 Bodensteiner,Leukocyte Marker and 3-5D minutes (2003) Count in blood products 15-CD4HIV Surface FIGS. 1-2 4 hours 10 Rodriguez (2005). AIDS Marker and 3-5Dminutes Dieye et al. (2005) 16-Leukemia Surface FIGS. 1-2 4 hours 10Drexler et al (1986) Panels-Very Marker and 3-5D minutes complex17-Bladder Surface FIGS. 1-2 4 hours 10 Ramakumar et al Cancer Markerand 3-5D minutes (1999) Screening in Lotan et al. (2009) Urine-Urinesample 18-HLA DR Surface FIGS. 1-2 4 hours 10 Hershman et al. Sepsis andMarker and 3-5D minutes (2005) Immunosuppression Perry et al (2003)19-RECAF Plasma FIGS. 1-2 4 hours 10 Moro et al. (2005). Protein forProtein and 6-8D minutes Canine and other Cancers 20-CytoImmun-Cervical4 hours 10 Hilfrich et al. Screening minutes (2008) 21-ProcalcitoninPlasma FIGS. 1-2 4 hours 10 Assicot et al. (Bead Based Protein and 6-8Dminutes (1993) Protein) + Christ-Crain et al. Feasibility (2004)

It should be understood that each of the steps of the method may take apredetermined period of time to perform, and in between these stepsthere may be incubation and/or waiting steps, which are not shown forthe sake of simplicity.

According to some embodiments, the volume of the specimen or sample isless than 200 μL, less than 100 μL, less than 50 μL, less than 25 μL orless than 11 μL.

Typically, the total sample volumes are in the range of 10 to 1000 μL,100 to 900 μL, 200 to 800 μL, 300 to 700 μL, 400 to 600 μL, or 420 to500 μL.

According to some embodiments, the volume of the treatment compositionchambers 106, 108, 110 (also called blisters) is from about 1 μL to 1000μL. According to other embodiments, the volume of the specimen is fromabout 10 μL to 200 μL. According to other embodiments, the volume of thespecimen is about 1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 140,160, 180, 200, 250, 300, 350, 400, 450, or 500 μL.

According to some embodiments, the volume of the treatment compositions120, 122, 124 is at most about 500 μL. According to other embodiments,the volume of the specimen is at most about 200 μL. According to otherembodiments, the volume of the specimen at most about 500, 450, 400,350, 300, 250, 200, 180, 160, 140, 120, 100, 90, 80, 70, 60, 50, 40, 30,20, 10, or 1 μL.

According to some embodiments, the volume of a reactant is at leastabout 1 μL. According to other embodiments, the volume of the specimenis from about 10 μL. According to other embodiments, the volume of thespecimen is at least about 1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100,120, 140, 160, 180, 200, 250, 300, 350, 400, 450, or 500 μL.

The sequence of transfer of the various treatment compositions may beimportant to the reaction sequence and is typically predefined.

The reading region 1450 (FIG. 14M-N) is configured and constructed forone or more evaluation steps. These may include any of the following, orcombinations thereof:

-   -   a) transfer of radiation there-through,    -   b) impinging radiation thereupon;    -   c) detecting reflected, refracted, and/or transmitted radiation,    -   d) detecting emitted radiation;    -   e) capturing one or more images thereof;    -   f) performing image analysis on the captured images;    -   g) measuring electrical characteristics of the treated specimen;    -   h) impinging sonic energy thereon;    -   i) detecting sonic energy therefrom; and    -   j) analyzing the outputs of any one or more of the above steps.

According to some embodiments, the cartridge is introduced into a systemas described in International patent application publication no.WO2011/128893 to Kasdan et al., incorporated herein by reference.

According to some embodiments; the apparatus may have on-board means forshowing a result, such as a colorimetric strip (not shown). Additionallyor alternatively, the results are displayed in a display unit, separateand remote from system 101.

The blood sample is typically whole blood recently removed from apatient. The whole blood comprises mainly red blood cells (also calledRBCs or erythrocytes), platelets and white blood cells (also calledleukocytes), including lymphocytes and neutrophils. Increased number ofneutrophils, especially activated neutrophils are normally found in theblood stream during the beginning (acute) phase of inflammation,particularly as a result of bacterial infection, environmental exposureand some cancers.

CD64 (Cluster of Differentiation 64) is a type of integral membraneglycoprotein known as an Fc receptor that binds monomeric IgG-typeantibodies with high affinity. Neutrophil CD64 expression quantificationprovides improved diagnostic detection of infection/sepsis compared withthe standard diagnostic tests used in current medical practice.

CD163 (Cluster of Differentiation 163) is a human protein encoded by theCD163 gene. It has also been shown to mark cells of monocyte/macrophagelineage.

Typically, the total sample volumes are in the range of 10 to 1000 μL,100 to 900 μL, 200 to 800 μL, 300 to 700 μL, 400 to 600 μL, or 420 to500 μL.

According to some embodiments, the volume of the treatment compositionchambers 106, 108, 110 (also called blisters) is from about 1 μL to 1000μL. According to other embodiments, the volume of the specimen is fromabout 10 μL, to 200 μL. According to other embodiments, the volume ofthe specimen is about 1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120,140, 160, 180, 200, 250, 300, 350, 400, 450, or 500 μL.

According to some embodiments, the volume of the treatment compositions120, 122, 124 is at most about 500 μL. According to other embodiments,the volume of the specimen is at most about 200 μL. According to otherembodiments, the volume of the specimen at most about 500, 450, 400,350, 300, 250, 200, 180, 160, 140, 120, 100, 90, 80, 70, 60, 50, 40, 30,20, 10, or 1 μL.

According to some embodiments, the volume of a reactant is at leastabout 1 μL. According to other embodiments, the volume of the specimenis from about 10 μL. According to other embodiments, the volume of thespecimen is at least about 1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100,120, 140, 160, 180, 200, 250, 300, 350, 400, 450, or 500 μL.

The time required to complete an assay using system 101 of the presentinvention varies depending on a number of factors, with non-limitingexamples that include described herein. In some embodiments, the timerequired to complete an assay is from about 0.5 to 100 minutes. In otherembodiments, the time required to complete an assay is from about 1 to20 minutes. In still other embodiments, the time required to complete anassay is from about 1 to 10 minutes. In some examples, the time requiredto complete an assay is from about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 25, 30, 35, 40, 50, 60, 80, or 100 minutes.

EXAMPLE Application No. 1—CD64 Infection & Sepsis

A cartridge 110 (FIG. 1A) is prepared for receiving a blood sample. Thecartridge comprises a number of treatment composition chambers 106, 108,110, adapted to respectively house a corresponding number of treatmentcompositions 120, 122, 124. These compositions are described in furtherdetail in U.S. Pat. No. 8,116,984 and in Davis, B H et al., (2006)),incorporated herein by reference. In brief, Reagent A comprises amixture of murine monoclonal antibodies (contains buffered saline),Reagent B—10× Concentrated Trillium Lyse solution (contains ammoniumchloride), Reagent C—suspension of 5.2 μm polystyrene beads labeled withStarfire Red and fluorescein isothiocyanate (FITC), (contains <0.1%sodium azide and 0.01% Tween 20).

TABLE 3 Time sequences of steps in the methodology of the presentinvention for detecting sepsis using CD64 and CD163 antibodies. LeukoDxdevice-present invention Volume Duration Step Description (uL) (min)comments 1 Mixing blood and Blood-10 antibodies Abs-50 4 2 Adding RBClysis 250 3 Might require buffer heating the buffer to 37C 3 Incubating,3 Vortexing 4 Adding 2 Less than 1 normalization beads 5 Reading Lessthan 1 Total 312 10

In the case of sepsis, by “normalization” is meant taking the ratio ofthe median of the target population fluorescence emission to the medianof the reference bead population fluorescence emission.

According to some embodiments, the readout may comprise anoptoelectronics core, which enables identification and detection offluorescent signals.

The CCD in the core, used for focusing, can also be used to readchemiluminescent signals. The readout to user may also indicate wherethe result falls relative to reference ranges.

The contents of these publications are incorporated by reference hereinwhere appropriate for teachings of additional or alternative details,features and/or technical background.

It is to be understood that the invention is not limited in itsapplication to the details set forth in the description contained hereinor illustrated in the drawings. The invention is capable of otherembodiments and of being practiced and carried out in various ways.Those skilled in the art will readily appreciate that variousmodifications and changes can be applied to the embodiments of theinvention as hereinbefore described without departing from its scope,defined in and by the appended claims.

REFERENCES

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1. A self-contained system for performing an assay for determining achemical state, the system comprising: a) a stationary cartridge forperforming the assay therein, the cartridge adapted to house at leastone reagent adapted to react with a sample; and at least one reporterfunctionality adapted to report a reaction of said at least one reagentwith said sample to report a result of said assay; wherein saidcartridge further comprises an alignment means adapted to align areading channel on said cartridge for a detection of said least onereporter functionality; b) a mechanical controller comprising; i. afirst urging means adapted to apply a force externally onto saidcartridge to release said at least one reagent; ii. at least one secondurging means adapted to apply a removable force to induce fluidicmovement in a first direction in said cartridge and upon removal of saidforce causing fluidic movement in an opposite direction to said firstdirection; c) an optical reader adapted to detect said reaction; and d)a processor adapted to receive data from said optical reader and toprocess said data to determine said chemical state.
 2. (canceled)
 3. Asystem according to claim 1, further comprising a plurality of fluidicopen channels, all said channels in liquid communication with eachother.
 4. A system according to claim 3, wherein said cartridge isadapted to be sealed after receiving a fluid specimen and to pass apredetermined quantity of said sample through at least part of saidplurality of fluidic open channels.
 5. A system according to claim 4,wherein said cartridge further comprises at least one inflatabledeformable elastic chamber adapted to apply at least one of a negativepressure and a positive pressure in said fluidic channels.
 6. A systemaccording to claim 5, wherein said at least one deformable elasticchamber is adapted to further contact said at least one reagent storedin a sealed on-board storage chamber with a predetermined quantity ofsaid sample in a reaction chamber to induce said reaction.
 7. A systemaccording to claim 6, wherein said a first urging means is disposedproximal to said on-board storage chamber such that upon movement isadapted to break a frangible seal on said storage chamber.
 8. A systemaccording to claim 7, wherein said alignment means adapted to align witha reading channel on said cartridge for a detection of a reaction insaid predetermined quantity of said sample.
 9. A system according toclaim 7, wherein some of said plurality of fluidic open channels are ofa cross-section of 0.1 to 2 mm².
 10. A system according to claim 8,wherein said predetermined quantity is of a volume of 10 to 500microliters.
 11. (canceled)
 12. A system according to claim 1, whereinsaid cartridge is adapted to induce cascaded sequential reactions of aplurality of on-board reagents, with said at least one of said sampleand a reaction product.
 13. A system according to claim 1, wherein saidcartridge comprises at least one reaction chamber of a volume of 200 to10000 microliters.
 14. A system according to claim 1, further comprisinga temperature control device external to said cartridge, said devicebeing adapted to control a temperature of said reaction. 15.-23.(canceled)
 24. A system according to claim 1, wherein said cartridge isa disposable microfluidics cartridge.
 25. A system according to claim 1,wherein said sample is introduced to said cartridge via capillaryaction. 26.-29. (canceled)
 30. A system according to claim 1, whereinsaid at least one reagent disposed in said cartridge comprises at leastone sepsis biomarker. 31.-58. (canceled)